diff --git a/LICENSE b/LICENSE index f84e7a59..003b1b62 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. 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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. diff --git a/deepcell/__init__.py b/deepcell/__init__.py index fcb5888e..c3548b3a 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 f5e0556e..db222fa7 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 5220a45b..0ea2c7cd 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 b33ddf44..c1e2f159 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 f2474c64..e67e3f23 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 2ef1e32c..20f0211f 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 3b4952e7..fa532d3c 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 91f9ada3..f9eb96c1 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 4a43aaf4..35e96dda 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 14b79884..c3e0f051 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 d69ca1c4..f78aeaf1 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 17c2d687..7ce6023c 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 64b03b18..0ec4d3fb 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 19ac4cea..b339ebcf 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 4f00ce37..43e67614 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 d19ba3d7..a91fa5a4 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 4b5e832f..07f788f2 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 d9686858..8ca6e631 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 ae13c393..b6128c1e 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 2c250256..975d8a76 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 e351b89b..411e8e22 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 457ee49c..d1c4d685 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 93a15ef7..7f9be343 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 7090821c..60589422 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 fbd820d4..59abbdf8 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 0436fb0b..28e3eade 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 d2abf592..107d8526 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 fc191b46..1d8a1e8b 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 3611ba40..0408d55e 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 1fe33c89..fb0da1fa 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 f674cb04..64883f70 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 7d98c27d..d387217f 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 778dc46d..edc5c4fa 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 33adfe1a..48b2a69b 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 536e6141..35f1951d 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 14516443..33341c98 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 4eb6d251..045ad1fe 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 dc39c77d..bdcb9554 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 3721f015..95bc33f8 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 ea90db58..53937cc7 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 49e582fd..62e54ee9 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 c5d88ce8..0b22a9e8 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 6d69bee1..59cad201 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 65a482ff..5b0c2fda 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 4350b019..02e3e903 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 b7ef7725..c1ec93dc 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 c531908d..e87e6cda 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 07649ed9..3cd5bc19 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 ec773d96..a2de6f5c 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 907d6f29..5a2a8950 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 c1d5a8e7..08a21b1c 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 aaeb69e4..202979fe 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 45de774f..fa8857a7 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 58be451a..8457994f 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 a4155510..b757c94e 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 747a90d8..d44544fb 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 e83cf54f..f22622b0 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 c99066be..fcf39f5f 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 37886c83..2f7d4caa 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 cc3a2213..87fa83e0 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 c81b6e71..4d338e80 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 4fc9fbcc..89c7b9dc 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 92a3578b..2fb39baf 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 26b9c3dd..aa941bbb 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 294004ce..ddc607de 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 ce5ca484..e9b60c37 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 65a0db1b..c1536116 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 7bc95d1d..990f3ee4 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 ce7dad3f..ca71698b 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 8520ef50..be806ec7 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 31503ea4..cbe1c915 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 fea1132b..32ba831f 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 262a8e43..73881732 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 3656d5f6..cd4ac738 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 179f701a..15945ee3 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 0e141b00..b3bd7028 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 31a984e2..49996232 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 9b3e7a10..95913be2 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 8fbd08c4..84f83424 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 d28ce544..53d8fac9 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 fba7cc1c..f48c9e78 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 887221a6..23e064d3 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 6373cae2..582201c7 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 50b68793..a2584a44 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 07d44828..f7275de5 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 8e26046d..6ce0d857 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 85ee3650..34f21e0c 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 4105b752..e2bfdebd 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 7608e61e..95ed4210 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 e537191e..6bea271a 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 315d6b54..49cc3c12 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