Remove line profile feature

Author: SylviaWhittle

notebooks/grainstats.py

@@ -182,7 +182,6 @@ def _(mo):
     grainstats:
       run: true # Options : true, false
       edge_detection_method: binary_erosion # Options: canny, binary erosion. Do not change this unless you are sure of what this will do.
-      extract_height_profile: true # Extract height profiles along maximum feret of molecules
       class_names: ["DNA", "Protein"] # The names corresponding to each class of a object identified, please specify merged classes after.
     plotting:
       run: true # Options : true, false

tests/__snapshots__/test_classes.ambr

@@ -107,11 +107,6 @@
       'total_branch_length': 12.3456789,
     }),
     'filename': 'dummy',
-    'height_profiles': dict({
-      1: dict({
-        0: array([1, 2, 3, 4, 5]),
-      }),
-    }),
     'image': array([[0.5213857 , 0.60384184, 0.4709418 , 0.20324795, 0.528759  ,
           0.19103628, 0.2815456 , 0.75368154, 0.5516718 , 0.8637221 ],
          [0.80537224, 0.24837266, 0.18985741, 0.98399556, 0.66999716,
@@ -929,7 +924,6 @@
           'Protein',
         ]),
         'edge_detection_method': 'binary_erosion',
-        'extract_height_profile': True,
         'run': True,
       }),
       'loading': dict({
@@ -1586,11 +1580,6 @@
           'total_branch_length': 12.3456789,
         }),
         'filename': 'example_catenanes',
-        'height_profiles': dict({
-          1: dict({
-            0: array([1, 2, 3, 4, 5]),
-          }),
-        }),
         'image': array([[-0.08690765, -0.08389194, -0.06598138, ...,  0.0110641 ,
           -0.00549059, -0.01650386],
          [-0.12658192, -0.08494661, -0.04653462, ...,  0.04816124,
@@ -1991,11 +1980,6 @@
           'total_branch_length': 12.3456789,
         }),
         'filename': 'example_catenanes',
-        'height_profiles': dict({
-          1: dict({
-            0: array([1, 2, 3, 4, 5]),
-          }),
-        }),
         'image': array([[-0.0217186 ,  0.02818649,  0.04690913, ...,  0.        ,
            0.        ,  0.        ],
          [-0.00605352,  0.01296311,  0.00851397, ...,  0.        ,
@@ -2526,7 +2510,6 @@
           'Protein',
         ]),
         'edge_detection_method': 'binary_erosion',
-        'extract_height_profile': True,
         'run': True,
       }),
       'loading': dict({
@@ -3183,11 +3166,6 @@
           'total_branch_length': 12.3456789,
         }),
         'filename': 'example_rep',
-        'height_profiles': dict({
-          1: dict({
-            0: array([1, 2, 3, 4, 5]),
-          }),
-        }),
         'image': array([[-0.02291669, -0.01486279,  0.0156244 , ...,  0.10213933,
            0.19618212,  0.32910987],
          [ 0.01603361,  0.01538401,  0.03241716, ...,  0.022104  ,

tests/__snapshots__/test_processing.ambr

@@ -893,16 +893,6 @@
           'total_branch_length': np.float64(8.572882640558748e-08),
         }),
         'filename': 'minicircle_small',
-        'height_profiles': dict({
-          '1': dict({
-            '0': array([1.13298136, 1.80644355, 2.05277056, 1.84378801, 1.4742514 ,
-         1.24258281, 1.33742077, 1.62488016, 1.91666981, 1.93168252,
-         1.67172504, 1.46181822, 1.44409109, 1.52838539, 1.61861484,
-         1.70554438, 1.59198594, 1.35754259, 1.01935129, 0.77867273,
-         0.7977643 , 1.10508701, 1.53874369, 1.83778951, 1.63307159,
-         0.95431994]),
-          }),
-        }),
         'image': array([[-1.61518513e-03,  1.71570210e-02,  6.46054637e-02,
            9.91101526e-02,  1.00360096e-01,  9.43137553e-02,
            9.34290351e-02,  9.15878578e-02,  6.17686398e-02,
@@ -2666,15 +2656,6 @@
           'total_branch_length': np.float64(7.305426523977305e-08),
         }),
         'filename': 'minicircle_small',
-        'height_profiles': dict({
-          '1': dict({
-            '0': array([0.92839707, 1.85075817, 2.03634558, 1.4346181 , 0.58507458,
-         0.14468474, 0.06565325, 0.19708489, 0.15940512, 0.12652616,
-         0.19245536, 0.46508443, 0.9546899 , 1.52486005, 1.95634547,
-         2.23783747, 2.34011511, 2.37861338, 2.33900584, 2.29793771,
-         2.15637048, 1.97662945, 1.51696556, 0.92431229]),
-          }),
-        }),
         'image': array([[-1.22458486e-02,  1.19310119e-01,  2.22751713e-01,
            2.91382109e-01,  3.41948057e-01,  3.71192639e-01,
            3.21788191e-01,  1.89744979e-01,  5.98432960e-02,
@@ -3991,15 +3972,6 @@
           'total_branch_length': np.float64(1.0331433269128837e-07),
         }),
         'filename': 'minicircle_small',
-        'height_profiles': dict({
-          '1': dict({
-            '0': array([0.9894515 , 1.7465862 , 1.80917238, 1.15014259, 0.45595278,
-         0.12635905, 0.21275054, 0.48902222, 0.70775335, 0.77421593,
-         0.65440809, 0.52278137, 0.42119907, 0.30709432, 0.4137407 ,
-         0.60326418, 0.89554341, 1.41572822, 1.85311755, 2.02674506,
-         1.81754884, 1.2429432 ]),
-          }),
-        }),
         'image': array([[-1.17980880e-01, -1.29790119e-01, -7.50836842e-02,
           -5.93735717e-02, -1.12717801e-01, -1.72709299e-01,
           -1.28303809e-01,  2.00624994e-02,  1.77433914e-01,

tests/conftest.py

@@ -622,7 +622,6 @@ def dummy_graincrop(
         thresholds=(1, 2),
         filename="dummy",
         stats={1: {0: {"centre_x": 5, "centre_y": 5}}},
-        height_profiles={1: {0: np.asarray([1, 2, 3, 4, 5])}},
         skeleton=dummy_skeleton,
         disordered_trace=dummy_disordered_trace,
         nodes={0: dummy_node, 1: dummy_node},
@@ -662,7 +661,6 @@ def graincrop_catenanes_0(
         thresholds=(1, 2),
         filename="example_catenanes",
         stats={1: {0: {"centre_x": 5, "centre_y": 5}}},
-        height_profiles={1: {0: np.asarray([1, 2, 3, 4, 5])}},
         skeleton=dummy_skeleton,
         disordered_trace=dummy_disordered_trace,
         nodes={0: dummy_node, 1: dummy_node},
@@ -690,7 +688,6 @@ def graincrop_catenanes_1(
         thresholds=(1, 2),
         filename="example_catenanes",
         stats={1: {0: {"centre_x": 5, "centre_y": 5}}},
-        height_profiles={1: {0: np.asarray([1, 2, 3, 4, 5])}},
         skeleton=dummy_skeleton,
         disordered_trace=dummy_disordered_trace,
         nodes={0: dummy_node, 1: dummy_node},
@@ -757,7 +754,6 @@ def graincrop_rep_int_0(
         thresholds=(1, 2),
         filename="example_rep",
         stats={1: {0: {"centre_x": 5, "centre_y": 5}}},
-        height_profiles={1: {0: np.asarray([1, 2, 3, 4, 5])}},
         skeleton=dummy_skeleton,
         disordered_trace=dummy_disordered_trace,
         nodes={0: dummy_node, 1: dummy_node},