From c00734da8886ffd8676fa4a297afa33427cc82b4 Mon Sep 17 00:00:00 2001 From: Ross Barnowski Date: Sat, 30 May 2026 11:22:08 -0700 Subject: [PATCH 1/2] LIC: Revert to exact OSI Apache2 text. --- LICENSE | 31 ++++++++++++++----------------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/LICENSE b/LICENSE index f84e7a594..003b1b62b 100644 --- a/LICENSE +++ b/LICENSE @@ -1,5 +1,7 @@ - Modified Apache License + + Apache License Version 2.0, January 2004 + http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION @@ -63,19 +65,18 @@ subsequently incorporated within the Work. 2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a non-commercial, - academic perpetual, worldwide, non-exclusive, no-charge, royalty-free, - irrevocable copyright license to reproduce, prepare Derivative Works - of, publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. For any other - use, including commercial use, please contact: vanvalenlab@gmail.com. + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. 3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a non-commercial, - academic perpetual, worldwide, non-exclusive, no-charge, royalty-free, - irrevocable (except as stated in this section) patent license to make, - have made, use, offer to sell, sell, import, and otherwise transfer the - Work, where such license applies only to those patent claims licensable + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable by such Contributor that are necessarily infringed by their Contribution(s) alone or by combination of their Contribution(s) with the Work to which such Contribution(s) was submitted. If You @@ -173,10 +174,6 @@ incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. - 10. Neither the name of Caltech nor the names of its contributors may be - used to endorse or promote products derived from this software without - specific prior written permission. - END OF TERMS AND CONDITIONS APPENDIX: How to apply the Apache License to your work. @@ -190,7 +187,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright 2026 Van Valen Lab, Caltech Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. From 4afe01d1622f2dab4ef06e18d9b5495f4c6a914c Mon Sep 17 00:00:00 2001 From: Ross Barnowski Date: Sat, 30 May 2026 11:43:58 -0700 Subject: [PATCH 2/2] Rm per-file license notices. --- deepcell/__init__.py | 25 ------------- deepcell/_version.py | 26 -------------- deepcell/applications/__init__.py | 25 ------------- deepcell/applications/application.py | 25 ------------- deepcell/applications/application_test.py | 25 ------------- deepcell/applications/cell_tracking.py | 25 ------------- deepcell/applications/cell_tracking_test.py | 25 ------------- .../applications/cytoplasm_segmentation.py | 25 ------------- .../cytoplasm_segmentation_test.py | 25 ------------- deepcell/applications/label_detection.py | 25 ------------- deepcell/applications/label_detection_test.py | 25 ------------- deepcell/applications/mesmer.py | 25 ------------- deepcell/applications/mesmer_test.py | 25 ------------- .../applications/multiplex_segmentation.py | 25 ------------- deepcell/applications/nuclear_segmentation.py | 25 ------------- .../applications/nuclear_segmentation_test.py | 25 ------------- deepcell/applications/scale_detection.py | 25 ------------- deepcell/applications/scale_detection_test.py | 25 ------------- deepcell/callbacks.py | 25 ------------- deepcell/callbacks_test.py | 25 ------------- deepcell/data/__init__.py | 25 ------------- deepcell/data/tracking.py | 25 ------------- deepcell/data/tracking_test.py | 25 ------------- deepcell/datasets/__init__.py | 25 ------------- deepcell/datasets/dataset.py | 25 ------------- deepcell/datasets/dataset_test.py | 25 ------------- deepcell/datasets/dynamic_nuclear_net.py | 36 ------------------- deepcell/datasets/spot_net.py | 30 ---------------- deepcell/datasets/tissue_net.py | 30 ---------------- deepcell/image_generators/__init__.py | 25 ------------- deepcell/image_generators/cropping.py | 25 ------------- .../image_generators/fully_convolutional.py | 25 ------------- .../image_generators/image_generators_test.py | 25 ------------- deepcell/image_generators/sample.py | 25 ------------- deepcell/image_generators/scale.py | 25 ------------- deepcell/image_generators/semantic.py | 25 ------------- deepcell/image_generators/tracking.py | 25 ------------- deepcell/layers/__init__.py | 25 ------------- deepcell/layers/location.py | 25 ------------- deepcell/layers/location_test.py | 25 ------------- deepcell/layers/normalization.py | 25 ------------- deepcell/layers/normalization_test.py | 25 ------------- deepcell/layers/padding.py | 25 ------------- deepcell/layers/padding_test.py | 25 ------------- deepcell/layers/pooling.py | 25 ------------- deepcell/layers/pooling_test.py | 25 ------------- deepcell/layers/temporal.py | 25 ------------- deepcell/layers/temporal_test.py | 25 ------------- deepcell/layers/tensor_product.py | 25 ------------- deepcell/layers/tensor_product_test.py | 25 ------------- deepcell/layers/upsample.py | 25 ------------- deepcell/layers/upsample_test.py | 25 ------------- deepcell/losses.py | 25 ------------- deepcell/losses_test.py | 25 ------------- deepcell/metrics.py | 25 ------------- deepcell/model_zoo/__init__.py | 25 ------------- deepcell/model_zoo/featurenet.py | 25 ------------- deepcell/model_zoo/featurenet_test.py | 25 ------------- deepcell/model_zoo/fpn.py | 25 ------------- deepcell/model_zoo/panopticnet.py | 25 ------------- deepcell/model_zoo/panopticnet_test.py | 25 ------------- deepcell/model_zoo/tracking.py | 25 ------------- deepcell/model_zoo/tracking_test.py | 25 ------------- deepcell/running.py | 25 ------------- deepcell/running_test.py | 25 ------------- deepcell/tracking.py | 25 ------------- deepcell/training.py | 25 ------------- deepcell/utils/__init__.py | 25 ------------- deepcell/utils/backbone_utils.py | 25 ------------- deepcell/utils/backbone_utils_test.py | 25 ------------- deepcell/utils/data_utils.py | 25 ------------- deepcell/utils/data_utils_test.py | 25 ------------- deepcell/utils/export_utils.py | 25 ------------- deepcell/utils/io_utils.py | 25 ------------- deepcell/utils/io_utils_test.py | 25 ------------- deepcell/utils/misc_utils.py | 25 ------------- deepcell/utils/misc_utils_test.py | 25 ------------- deepcell/utils/plot_utils.py | 25 ------------- deepcell/utils/plot_utils_test.py | 25 ------------- deepcell/utils/tfrecord_utils.py | 25 ------------- deepcell/utils/tfrecord_utils_test.py | 25 ------------- deepcell/utils/tracking_utils.py | 25 ------------- deepcell/utils/train_utils.py | 25 ------------- deepcell/utils/train_utils_test.py | 25 ------------- deepcell/utils/transform_utils.py | 25 ------------- deepcell/utils/transform_utils_test.py | 25 ------------- docs/source/API-key.rst | 2 +- docs/source/datasets/dynamicnuclearnet.py | 3 +- docs/source/datasets/spotnet.py | 3 +- docs/source/datasets/tissuenet.py | 5 ++- setup.py | 25 ------------- 91 files changed, 5 insertions(+), 2205 deletions(-) diff --git a/deepcell/__init__.py b/deepcell/__init__.py index fcb5888e7..c3548b3a0 100644 --- a/deepcell/__init__.py +++ b/deepcell/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Package for single cell image segmentation with convolutional neural networks""" diff --git a/deepcell/_version.py b/deepcell/_version.py index f5e0556ea..db222fa72 100644 --- a/deepcell/_version.py +++ b/deepcell/_version.py @@ -1,29 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== - __title__ = 'DeepCell' __description__ = 'Deep learning for single cell image segmentation' __url__ = 'https://github.com/vanvalenlab/deepcell-tf' diff --git a/deepcell/applications/__init__.py b/deepcell/applications/__init__.py index 5220a45b1..0ea2c7cd5 100644 --- a/deepcell/applications/__init__.py +++ b/deepcell/applications/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Deepcell Applications - Pre-trained models for specific functions""" diff --git a/deepcell/applications/application.py b/deepcell/applications/application.py index b33ddf446..c1e2f1599 100644 --- a/deepcell/applications/application.py +++ b/deepcell/applications/application.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Base class for applications""" diff --git a/deepcell/applications/application_test.py b/deepcell/applications/application_test.py index f2474c64f..e67e3f23b 100644 --- a/deepcell/applications/application_test.py +++ b/deepcell/applications/application_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for Application""" diff --git a/deepcell/applications/cell_tracking.py b/deepcell/applications/cell_tracking.py index 2ef1e32cf..20f0211ff 100644 --- a/deepcell/applications/cell_tracking.py +++ b/deepcell/applications/cell_tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """A model that can detect whether 2 cells are same, different, or related.""" diff --git a/deepcell/applications/cell_tracking_test.py b/deepcell/applications/cell_tracking_test.py index 3b4952e7a..fa532d3c4 100644 --- a/deepcell/applications/cell_tracking_test.py +++ b/deepcell/applications/cell_tracking_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for CellTracking Application""" diff --git a/deepcell/applications/cytoplasm_segmentation.py b/deepcell/applications/cytoplasm_segmentation.py index 91f9ada33..f9eb96c16 100644 --- a/deepcell/applications/cytoplasm_segmentation.py +++ b/deepcell/applications/cytoplasm_segmentation.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Cytoplasmic segmentation application""" diff --git a/deepcell/applications/cytoplasm_segmentation_test.py b/deepcell/applications/cytoplasm_segmentation_test.py index 4a43aaf41..35e96dda5 100644 --- a/deepcell/applications/cytoplasm_segmentation_test.py +++ b/deepcell/applications/cytoplasm_segmentation_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for CytoplasmSegmentationModel""" diff --git a/deepcell/applications/label_detection.py b/deepcell/applications/label_detection.py index 14b79884b..c3e0f051b 100644 --- a/deepcell/applications/label_detection.py +++ b/deepcell/applications/label_detection.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Classify the type of an input image to send the data to the correct model""" diff --git a/deepcell/applications/label_detection_test.py b/deepcell/applications/label_detection_test.py index d69ca1c4a..f78aeaf1d 100644 --- a/deepcell/applications/label_detection_test.py +++ b/deepcell/applications/label_detection_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for LabelDetectionModel""" diff --git a/deepcell/applications/mesmer.py b/deepcell/applications/mesmer.py index 17c2d6871..7ce6023c7 100644 --- a/deepcell/applications/mesmer.py +++ b/deepcell/applications/mesmer.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Mesmer application""" diff --git a/deepcell/applications/mesmer_test.py b/deepcell/applications/mesmer_test.py index 64b03b183..0ec4d3fbf 100644 --- a/deepcell/applications/mesmer_test.py +++ b/deepcell/applications/mesmer_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for Mesmer Application""" diff --git a/deepcell/applications/multiplex_segmentation.py b/deepcell/applications/multiplex_segmentation.py index 19ac4ceac..b339ebcff 100644 --- a/deepcell/applications/multiplex_segmentation.py +++ b/deepcell/applications/multiplex_segmentation.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Multiplex segmentation application. Deprecated in favor of ``deepcell.applications.Mesmer`` instead. diff --git a/deepcell/applications/nuclear_segmentation.py b/deepcell/applications/nuclear_segmentation.py index 4f00ce37d..43e676146 100644 --- a/deepcell/applications/nuclear_segmentation.py +++ b/deepcell/applications/nuclear_segmentation.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Nuclear segmentation application""" diff --git a/deepcell/applications/nuclear_segmentation_test.py b/deepcell/applications/nuclear_segmentation_test.py index d19ba3d7f..a91fa5a4f 100644 --- a/deepcell/applications/nuclear_segmentation_test.py +++ b/deepcell/applications/nuclear_segmentation_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for NuclearSegmentationApplication""" diff --git a/deepcell/applications/scale_detection.py b/deepcell/applications/scale_detection.py index 4b5e832fa..07f788f22 100644 --- a/deepcell/applications/scale_detection.py +++ b/deepcell/applications/scale_detection.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Detect the scale of input data for rescaling for other models""" diff --git a/deepcell/applications/scale_detection_test.py b/deepcell/applications/scale_detection_test.py index d9686858b..8ca6e6311 100644 --- a/deepcell/applications/scale_detection_test.py +++ b/deepcell/applications/scale_detection_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for ScaleDetectionModel""" diff --git a/deepcell/callbacks.py b/deepcell/callbacks.py index ae13c3931..b6128c1e7 100644 --- a/deepcell/callbacks.py +++ b/deepcell/callbacks.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Custom Callbacks for DeepCell""" diff --git a/deepcell/callbacks_test.py b/deepcell/callbacks_test.py index 2c2502564..975d8a769 100644 --- a/deepcell/callbacks_test.py +++ b/deepcell/callbacks_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Custom Callbacks for DeepCell""" diff --git a/deepcell/data/__init__.py b/deepcell/data/__init__.py index e351b89b0..411e8e223 100644 --- a/deepcell/data/__init__.py +++ b/deepcell/data/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Data utilities using ``tf.data``.""" diff --git a/deepcell/data/tracking.py b/deepcell/data/tracking.py index 457ee49c0..d1c4d6858 100644 --- a/deepcell/data/tracking.py +++ b/deepcell/data/tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Dataset Builders""" diff --git a/deepcell/data/tracking_test.py b/deepcell/data/tracking_test.py index 93a15ef7a..7f9be3431 100644 --- a/deepcell/data/tracking_test.py +++ b/deepcell/data/tracking_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for tracking functions""" diff --git a/deepcell/datasets/__init__.py b/deepcell/datasets/__init__.py index 7090821c4..605894223 100644 --- a/deepcell/datasets/__init__.py +++ b/deepcell/datasets/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Builtin Datasets""" from .dynamic_nuclear_net import ( diff --git a/deepcell/datasets/dataset.py b/deepcell/datasets/dataset.py index fbd820d42..59abbdf87 100644 --- a/deepcell/datasets/dataset.py +++ b/deepcell/datasets/dataset.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Builtin Datasets""" diff --git a/deepcell/datasets/dataset_test.py b/deepcell/datasets/dataset_test.py index 0436fb0b0..28e3eadea 100644 --- a/deepcell/datasets/dataset_test.py +++ b/deepcell/datasets/dataset_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== import os import numpy as np diff --git a/deepcell/datasets/dynamic_nuclear_net.py b/deepcell/datasets/dynamic_nuclear_net.py index d2abf592b..107d85264 100644 --- a/deepcell/datasets/dynamic_nuclear_net.py +++ b/deepcell/datasets/dynamic_nuclear_net.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Timelapse datasets of a nuclear label including the raw images and ground truth segmentation masks annotated to track cell lineages""" @@ -58,10 +33,6 @@ class DynamicNuclearNetSegmentation(SegmentationDataset): def __init__(self, version="1.1"): """This dataset contains the segmentation portion of the DynamicNuclearNet dataset - This dataset is licensed under a modified Apache license for non-commercial academic - use only - http://www.github.com/vanvalenlab/deepcell-tf/LICENSE - Change Log - DynamicNuclearNet 1.0 (June 2023): The original dataset used for all experiments in Schwartz et al. 2023 @@ -101,10 +72,6 @@ def __init__(self, version="1.1"): - lineages: lineage records including the cell id, frames present and division links from parent to daughter cells - This dataset is licensed under a modified Apache license for non-commercial academic - use only - http://www.github.com/vanvalenlab/deepcell-tf/LICENSE - Change Log - DynamicNuclearNet 1.0 (June 2023): The original dataset used for all experiments in Schwartz et al. 2023 @@ -139,9 +106,6 @@ def __init__(self, version="1.1"): class DynamicNuclearNetSample(SegmentationDataset): """A 10 frame movie from DynamicNuclearNet with the raw fluorescent data and nuclear segmentation masks - - This dataset is licensed under a modified Apache license for non-commercial academic - use only http://www.github.com/vanvalenlab/deepcell-tf/LICENSE """ def __init__(self): super().__init__( diff --git a/deepcell/datasets/spot_net.py b/deepcell/datasets/spot_net.py index fc191b465..1d8a1e8bd 100644 --- a/deepcell/datasets/spot_net.py +++ b/deepcell/datasets/spot_net.py @@ -1,29 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== - import os import numpy as np @@ -57,10 +31,6 @@ def __init__(self, version="1.1"): - The test split is composed of 94 images, each of which are 128x128 pixels. See Laubscher et al. (2023) for details on image sources. - This dataset is licensed under a modified Apache license for non-commercial academic - use only - http://www.github.com/vanvalenlab/deepcell-tf/LICENSE - Change Log - SpotNet 1.0 (Aug 2023): The original dataset used for all experiments in Laubscher et al. (2023) diff --git a/deepcell/datasets/tissue_net.py b/deepcell/datasets/tissue_net.py index 3611ba40d..0408d55e6 100644 --- a/deepcell/datasets/tissue_net.py +++ b/deepcell/datasets/tissue_net.py @@ -1,29 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== - from deepcell.datasets.dataset import SegmentationDataset @@ -60,10 +34,6 @@ def __init__(self, version="1.1"): 256x256, we reshape these 512x512 images into 256x256 images, resulting in aproximately 1200 images. - This dataset is licensed under a modified Apache license for non-commercial academic - use only - http://www.github.com/vanvalenlab/deepcell-tf/LICENSE - Change Log - TissueNet 1.0 (July 2021): The original dataset used for all experiments in Greenwald, Miller at al. diff --git a/deepcell/image_generators/__init__.py b/deepcell/image_generators/__init__.py index 1fe33c89f..fb0da1fab 100644 --- a/deepcell/image_generators/__init__.py +++ b/deepcell/image_generators/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """ Custom Image Data Generators used to generate augmented batches of training data. These custom generators extend the keras.ImageDataGenerator, and allow diff --git a/deepcell/image_generators/cropping.py b/deepcell/image_generators/cropping.py index f674cb04a..64883f709 100644 --- a/deepcell/image_generators/cropping.py +++ b/deepcell/image_generators/cropping.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Semantic segmentation data generators with cropping.""" diff --git a/deepcell/image_generators/fully_convolutional.py b/deepcell/image_generators/fully_convolutional.py index 7d98c27da..d387217ff 100644 --- a/deepcell/image_generators/fully_convolutional.py +++ b/deepcell/image_generators/fully_convolutional.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Fully convolutional data generators. These data generators allow for training on augmented label masks (y) diff --git a/deepcell/image_generators/image_generators_test.py b/deepcell/image_generators/image_generators_test.py index 778dc46d9..edc5c4fa0 100644 --- a/deepcell/image_generators/image_generators_test.py +++ b/deepcell/image_generators/image_generators_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for custom image data generators""" diff --git a/deepcell/image_generators/sample.py b/deepcell/image_generators/sample.py index 33adfe1a0..48b2a69b7 100644 --- a/deepcell/image_generators/sample.py +++ b/deepcell/image_generators/sample.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Sample based data generators. Sample data generators yield data from a sliding window in order to categorize diff --git a/deepcell/image_generators/scale.py b/deepcell/image_generators/scale.py index 536e6141a..35f1951d5 100644 --- a/deepcell/image_generators/scale.py +++ b/deepcell/image_generators/scale.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Scale data generators. These generators perform random zooming on the raw data, and yield each image diff --git a/deepcell/image_generators/semantic.py b/deepcell/image_generators/semantic.py index 145164430..33341c98f 100755 --- a/deepcell/image_generators/semantic.py +++ b/deepcell/image_generators/semantic.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Semantic segmentation data generators.""" diff --git a/deepcell/image_generators/tracking.py b/deepcell/image_generators/tracking.py index 4eb6d2519..045ad1fec 100644 --- a/deepcell/image_generators/tracking.py +++ b/deepcell/image_generators/tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tracking data generators.""" diff --git a/deepcell/layers/__init__.py b/deepcell/layers/__init__.py index dc39c77d9..bdcb95544 100644 --- a/deepcell/layers/__init__.py +++ b/deepcell/layers/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Custom Layers""" from deepcell.layers import location diff --git a/deepcell/layers/location.py b/deepcell/layers/location.py index 3721f0156..95bc33f8f 100644 --- a/deepcell/layers/location.py +++ b/deepcell/layers/location.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Layers to encode location data""" diff --git a/deepcell/layers/location_test.py b/deepcell/layers/location_test.py index ea90db585..53937cc7b 100644 --- a/deepcell/layers/location_test.py +++ b/deepcell/layers/location_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the location layers""" from keras import testing_utils diff --git a/deepcell/layers/normalization.py b/deepcell/layers/normalization.py index 49e582fda..62e54ee92 100644 --- a/deepcell/layers/normalization.py +++ b/deepcell/layers/normalization.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Layers to noramlize input images for 2D and 3D images""" diff --git a/deepcell/layers/normalization_test.py b/deepcell/layers/normalization_test.py index c5d88ce88..0b22a9e8c 100644 --- a/deepcell/layers/normalization_test.py +++ b/deepcell/layers/normalization_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the normalization layers""" from absl.testing import parameterized diff --git a/deepcell/layers/padding.py b/deepcell/layers/padding.py index 6d69bee10..59cad2018 100644 --- a/deepcell/layers/padding.py +++ b/deepcell/layers/padding.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Layers for padding for 2D and 3D images""" diff --git a/deepcell/layers/padding_test.py b/deepcell/layers/padding_test.py index 65a482ff8..5b0c2fda1 100644 --- a/deepcell/layers/padding_test.py +++ b/deepcell/layers/padding_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for padding layers.""" diff --git a/deepcell/layers/pooling.py b/deepcell/layers/pooling.py index 4350b019e..02e3e9033 100644 --- a/deepcell/layers/pooling.py +++ b/deepcell/layers/pooling.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Layers to encode location data""" diff --git a/deepcell/layers/pooling_test.py b/deepcell/layers/pooling_test.py index b7ef7725d..c1ec93dca 100644 --- a/deepcell/layers/pooling_test.py +++ b/deepcell/layers/pooling_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the pooling layers""" from absl.testing import parameterized diff --git a/deepcell/layers/temporal.py b/deepcell/layers/temporal.py index c531908d0..e87e6cdac 100644 --- a/deepcell/layers/temporal.py +++ b/deepcell/layers/temporal.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/tf-keras-retinanet/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Upsampling layers""" import tensorflow as tf diff --git a/deepcell/layers/temporal_test.py b/deepcell/layers/temporal_test.py index 07649ed99..3cd5bc199 100644 --- a/deepcell/layers/temporal_test.py +++ b/deepcell/layers/temporal_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the upsampling layers""" import numpy as np diff --git a/deepcell/layers/tensor_product.py b/deepcell/layers/tensor_product.py index ec773d969..a2de6f5c8 100644 --- a/deepcell/layers/tensor_product.py +++ b/deepcell/layers/tensor_product.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Layers to generate tensor products for 2D and 3D data""" diff --git a/deepcell/layers/tensor_product_test.py b/deepcell/layers/tensor_product_test.py index 907d6f29b..5a2a89506 100644 --- a/deepcell/layers/tensor_product_test.py +++ b/deepcell/layers/tensor_product_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the tensor product layers""" import numpy as np diff --git a/deepcell/layers/upsample.py b/deepcell/layers/upsample.py index c1d5a8e74..08a21b1ce 100644 --- a/deepcell/layers/upsample.py +++ b/deepcell/layers/upsample.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/tf-keras-retinanet/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Upsampling layers""" import tensorflow as tf diff --git a/deepcell/layers/upsample_test.py b/deepcell/layers/upsample_test.py index aaeb69e4e..202979fe6 100644 --- a/deepcell/layers/upsample_test.py +++ b/deepcell/layers/upsample_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for the upsampling layers""" import numpy as np diff --git a/deepcell/losses.py b/deepcell/losses.py index 45de774f1..fa8857a70 100644 --- a/deepcell/losses.py +++ b/deepcell/losses.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Custom loss functions for DeepCell""" diff --git a/deepcell/losses_test.py b/deepcell/losses_test.py index 58be451ae..8457994f0 100644 --- a/deepcell/losses_test.py +++ b/deepcell/losses_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for custom loss functions""" diff --git a/deepcell/metrics.py b/deepcell/metrics.py index a41555101..b757c94ef 100644 --- a/deepcell/metrics.py +++ b/deepcell/metrics.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Metrics have been moved to deepcell_toolbox.metrics.""" from deepcell_toolbox.metrics import PixelMetrics diff --git a/deepcell/model_zoo/__init__.py b/deepcell/model_zoo/__init__.py index 747a90d89..d44544fb3 100644 --- a/deepcell/model_zoo/__init__.py +++ b/deepcell/model_zoo/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Deepcell Model Zoo Module""" diff --git a/deepcell/model_zoo/featurenet.py b/deepcell/model_zoo/featurenet.py index e83cf54f1..f22622b05 100644 --- a/deepcell/model_zoo/featurenet.py +++ b/deepcell/model_zoo/featurenet.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Assortment of CNN architectures for single cell segmentation""" diff --git a/deepcell/model_zoo/featurenet_test.py b/deepcell/model_zoo/featurenet_test.py index c99066be4..fcf39f5f2 100644 --- a/deepcell/model_zoo/featurenet_test.py +++ b/deepcell/model_zoo/featurenet_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Test the featurenet models.""" diff --git a/deepcell/model_zoo/fpn.py b/deepcell/model_zoo/fpn.py index 37886c839..2f7d4caa0 100644 --- a/deepcell/model_zoo/fpn.py +++ b/deepcell/model_zoo/fpn.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Feature pyramid network utility functions""" diff --git a/deepcell/model_zoo/panopticnet.py b/deepcell/model_zoo/panopticnet.py index cc3a2213e..87fa83e04 100755 --- a/deepcell/model_zoo/panopticnet.py +++ b/deepcell/model_zoo/panopticnet.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Feature pyramid network utility functions""" diff --git a/deepcell/model_zoo/panopticnet_test.py b/deepcell/model_zoo/panopticnet_test.py index c81b6e715..4d338e804 100644 --- a/deepcell/model_zoo/panopticnet_test.py +++ b/deepcell/model_zoo/panopticnet_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Test the RetinaMask models.""" diff --git a/deepcell/model_zoo/tracking.py b/deepcell/model_zoo/tracking.py index 4fc9fbcc1..89c7b9dcd 100644 --- a/deepcell/model_zoo/tracking.py +++ b/deepcell/model_zoo/tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Assortment of CNN (and GNN) architectures for tracking single cells""" diff --git a/deepcell/model_zoo/tracking_test.py b/deepcell/model_zoo/tracking_test.py index 92a3578b8..2fb39baf9 100644 --- a/deepcell/model_zoo/tracking_test.py +++ b/deepcell/model_zoo/tracking_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Test the tracking models.""" diff --git a/deepcell/running.py b/deepcell/running.py index 26b9c3dde..aa941bbb3 100644 --- a/deepcell/running.py +++ b/deepcell/running.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for running convolutional neural networks""" diff --git a/deepcell/running_test.py b/deepcell/running_test.py index 294004ce8..ddc607dee 100644 --- a/deepcell/running_test.py +++ b/deepcell/running_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for running functions """ diff --git a/deepcell/tracking.py b/deepcell/tracking.py index ce5ca4848..e9b60c373 100644 --- a/deepcell/tracking.py +++ b/deepcell/tracking.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """A cell tracking class capable of extending labels across sequential frames.""" diff --git a/deepcell/training.py b/deepcell/training.py index 65a0db1bf..c15361161 100644 --- a/deepcell/training.py +++ b/deepcell/training.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for training convolutional neural networks""" diff --git a/deepcell/utils/__init__.py b/deepcell/utils/__init__.py index 7bc95d1dd..990f3ee4f 100644 --- a/deepcell/utils/__init__.py +++ b/deepcell/utils/__init__.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Deepcell Utilities Module""" diff --git a/deepcell/utils/backbone_utils.py b/deepcell/utils/backbone_utils.py index ce7dad3f4..ca71698b5 100644 --- a/deepcell/utils/backbone_utils.py +++ b/deepcell/utils/backbone_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for creating model backbones""" diff --git a/deepcell/utils/backbone_utils_test.py b/deepcell/utils/backbone_utils_test.py index 8520ef505..be806ec75 100644 --- a/deepcell/utils/backbone_utils_test.py +++ b/deepcell/utils/backbone_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for backbone_utils""" diff --git a/deepcell/utils/data_utils.py b/deepcell/utils/data_utils.py index 31503ea4c..cbe1c9152 100644 --- a/deepcell/utils/data_utils.py +++ b/deepcell/utils/data_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for making training data""" diff --git a/deepcell/utils/data_utils_test.py b/deepcell/utils/data_utils_test.py index fea1132be..32ba831f5 100644 --- a/deepcell/utils/data_utils_test.py +++ b/deepcell/utils/data_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for data_utils""" import os diff --git a/deepcell/utils/export_utils.py b/deepcell/utils/export_utils.py index 262a8e435..73881732e 100644 --- a/deepcell/utils/export_utils.py +++ b/deepcell/utils/export_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Save Keras models as a SavedModel for TensorFlow Serving""" diff --git a/deepcell/utils/io_utils.py b/deepcell/utils/io_utils.py index 3656d5f6b..cd4ac7384 100644 --- a/deepcell/utils/io_utils.py +++ b/deepcell/utils/io_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for reading/writing files""" diff --git a/deepcell/utils/io_utils_test.py b/deepcell/utils/io_utils_test.py index 179f701a3..15945ee36 100644 --- a/deepcell/utils/io_utils_test.py +++ b/deepcell/utils/io_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for io_utils""" import os diff --git a/deepcell/utils/misc_utils.py b/deepcell/utils/misc_utils.py index 0e141b004..b3bd70289 100644 --- a/deepcell/utils/misc_utils.py +++ b/deepcell/utils/misc_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Miscellaneous utility functions""" diff --git a/deepcell/utils/misc_utils_test.py b/deepcell/utils/misc_utils_test.py index 31a984e26..499962320 100644 --- a/deepcell/utils/misc_utils_test.py +++ b/deepcell/utils/misc_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for misc_utils""" from tensorflow.python.platform import test diff --git a/deepcell/utils/plot_utils.py b/deepcell/utils/plot_utils.py index 9b3e7a10c..95913be2d 100644 --- a/deepcell/utils/plot_utils.py +++ b/deepcell/utils/plot_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities plotting data""" diff --git a/deepcell/utils/plot_utils_test.py b/deepcell/utils/plot_utils_test.py index 8fbd08c43..84f83424a 100644 --- a/deepcell/utils/plot_utils_test.py +++ b/deepcell/utils/plot_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for io_utils""" import pytest diff --git a/deepcell/utils/tfrecord_utils.py b/deepcell/utils/tfrecord_utils.py index d28ce5448..53d8fac9d 100644 --- a/deepcell/utils/tfrecord_utils.py +++ b/deepcell/utils/tfrecord_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Functions for reading and writing segmentation datasets as TF Records""" diff --git a/deepcell/utils/tfrecord_utils_test.py b/deepcell/utils/tfrecord_utils_test.py index fba7cc1c5..f48c9e780 100644 --- a/deepcell/utils/tfrecord_utils_test.py +++ b/deepcell/utils/tfrecord_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-toolbox/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================ """Tests for tfrecord utils""" import numpy as np diff --git a/deepcell/utils/tracking_utils.py b/deepcell/utils/tracking_utils.py index 887221a66..23e064d37 100644 --- a/deepcell/utils/tracking_utils.py +++ b/deepcell/utils/tracking_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 David Van Valen at California Institute of Technology -# (Caltech), with support from the Paul Allen Family Foundation, Google, -# & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for tracking cells""" diff --git a/deepcell/utils/train_utils.py b/deepcell/utils/train_utils.py index 6373cae2e..582201c73 100644 --- a/deepcell/utils/train_utils.py +++ b/deepcell/utils/train_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for training neural nets""" diff --git a/deepcell/utils/train_utils_test.py b/deepcell/utils/train_utils_test.py index 50b687934..a2584a442 100644 --- a/deepcell/utils/train_utils_test.py +++ b/deepcell/utils/train_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for train_utils""" import os diff --git a/deepcell/utils/transform_utils.py b/deepcell/utils/transform_utils.py index 07d448286..f7275de5e 100644 --- a/deepcell/utils/transform_utils.py +++ b/deepcell/utils/transform_utils.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Utilities for data transformations""" diff --git a/deepcell/utils/transform_utils_test.py b/deepcell/utils/transform_utils_test.py index 8e26046d0..6ce0d857d 100644 --- a/deepcell/utils/transform_utils_test.py +++ b/deepcell/utils/transform_utils_test.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== """Tests for transform_utils""" import numpy as np diff --git a/docs/source/API-key.rst b/docs/source/API-key.rst index 85ee3650e..34f21e0c0 100644 --- a/docs/source/API-key.rst +++ b/docs/source/API-key.rst @@ -1,7 +1,7 @@ DeepCell API Key ================ -DeepCell models and training datasets are licensed under a `modified Apache license `_ for non-commercial academic use only. An API key for accessing datasets and models can be obtained at https://users.deepcell.org/login/. +DeepCell models and training datasets are licensed under a modified Apache license for non-commercial academic use only. An API key for accessing datasets and models can be obtained at https://users.deepcell.org/login/. For more information about datasets published through DeepCell, please see :doc:`/data-gallery/index`. diff --git a/docs/source/datasets/dynamicnuclearnet.py b/docs/source/datasets/dynamicnuclearnet.py index 4105b7529..e2bfdebd8 100644 --- a/docs/source/datasets/dynamicnuclearnet.py +++ b/docs/source/datasets/dynamicnuclearnet.py @@ -10,8 +10,7 @@ Schwartz et al. 2023. The dataset is made up of two subsets, one for tracking and one for segmentation. -This dataset is licensed under a `modified Apache license -`_ for non-commercial +This dataset is licensed under a modified Apache license for non-commercial academic use only The dataset can be accessed using `deepcell.datasets` with a DeepCell API key. diff --git a/docs/source/datasets/spotnet.py b/docs/source/datasets/spotnet.py index 7608e61ed..95ed42107 100644 --- a/docs/source/datasets/spotnet.py +++ b/docs/source/datasets/spotnet.py @@ -9,8 +9,7 @@ SpotNet is a training dataset for a deep learning model for spot detection published in Laubscher et al. 2023. -This dataset is licensed under a `modified Apache license -`_ for non-commercial +This dataset is licensed under a `modified Apache license for non-commercial academic use only. The dataset can be accessed using `deepcell.datasets` with a DeepCell API key. diff --git a/docs/source/datasets/tissuenet.py b/docs/source/datasets/tissuenet.py index e537191ed..6bea271ae 100644 --- a/docs/source/datasets/tissuenet.py +++ b/docs/source/datasets/tissuenet.py @@ -33,8 +33,7 @@ * TissueNet 1.1 (April 2022): This version of TissueNet has gone through an additional round of manual QC to ensure consistency in labeling across the entire dataset. -This dataset is licensed under a `modified Apache license -`_ for non-commercial +This dataset is licensed under a modified Apache license for non-commercial academic use only The dataset can be accessed using `deepcell.datasets` with a DeepCell API key. @@ -47,4 +46,4 @@ tissuenet = TissueNet(version='1.1') X_val, y_val, meta_val = tissuenet.load_data(split='val') -# sphinx_gallery_thumbnail_path = '../images/multiplex_overlay.png' \ No newline at end of file +# sphinx_gallery_thumbnail_path = '../images/multiplex_overlay.png' diff --git a/setup.py b/setup.py index 315d6b54e..49cc3c12c 100644 --- a/setup.py +++ b/setup.py @@ -1,28 +1,3 @@ -# Copyright 2016-2024 The Van Valen Lab at the California Institute of -# Technology (Caltech), with support from the Paul Allen Family Foundation, -# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01. -# All rights reserved. -# -# Licensed under a modified Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.github.com/vanvalenlab/deepcell-tf/LICENSE -# -# The Work provided may be used for non-commercial academic purposes only. -# For any other use of the Work, including commercial use, please contact: -# vanvalenlab@gmail.com -# -# Neither the name of Caltech nor the names of its contributors may be used -# to endorse or promote products derived from this software without specific -# prior written permission. -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# ============================================================================== import os from codecs import open