feat: section gap augmentation

Author: torms3

deepem/data/augment/cortex/aug_16nm.py

@@ -10,6 +10,8 @@ def get_augmentation(
     random=False,
     recompute=False,
     border=[],
+    section_gap=0,
+    mask_section_gap=False,
     **kwargs
 ):
     augs = list()
@@ -92,4 +94,8 @@ def get_augmentation(
     if recompute:
         augs.append(Label(targets=recompute))
 
+    # Section gap
+    if section_gap > 0:
+        augs.append(SectionGap(num_secs=section_gap, masked=mask_section_gap))
+
     return Compose(augs)

deepem/data/augment/cortex/aug_16nm_gap3-5.py

@@ -0,0 +1,104 @@
+from augmentor import *
+
+
+def get_augmentation(
+    is_train,
+    box=None,
+    missing=7,
+    blur=7,
+    lost=True,
+    random=False,
+    recompute=False,
+    border=[],
+    **kwargs
+):
+    augs = list()
+
+    # Box
+    if is_train:
+        if box == 'noise':
+            augs.append(
+                NoiseBox(sigma=(1, 3), dims=(3, 13), margin=(1, 3, 3),
+                         density=0.3, skip=0.1)
+            )
+        elif box == 'fill':
+            augs.append(
+                FillBox(dims=(3, 13), margin=(1, 3, 3),
+                        density=0.3, skip=0.1)
+            )
+
+    # Brightness & contrast purterbation
+    augs.append(
+        MixedGrayscale2D(
+            contrast_factor=0.5,
+            brightness_factor=0.5,
+            prob=1, skip=0.3))
+
+    # Missing section & misalignment
+    to_blend = list()
+    # Misalingments
+    trans = Compose([Misalign((0,  3), margin=1),
+                     Misalign((0,  8), margin=1),
+                     Misalign((0, 13), margin=1)])
+
+    # Out-of-alignments
+    slip = Compose([SlipMisalign((0,  3), interp=True, margin=1),
+                    SlipMisalign((0,  8), interp=True, margin=1),
+                    SlipMisalign((0, 13), interp=True, margin=1)])
+    to_blend.append(Blend([trans, slip], props=[0.7, 0.3]))
+    if is_train:
+        to_blend.append(Blend([
+            MisalignPlusMissing((2, 8), value=0, random=random),
+            MisalignPlusMissing((2, 8), value=0, random=False)
+        ]))
+    else:
+        to_blend.append(MisalignPlusMissing((2, 8), value=0, random=False))
+    if missing > 0:
+        if is_train:
+            to_blend.append(Blend([
+                MixedMissingSection(maxsec=missing, individual=True, value=0, random=False),
+                MixedMissingSection(maxsec=missing, individual=True, value=0, random=random),
+                MissingSection(maxsec=missing, individual=False, value=0, random=random),
+            ]))
+        else:
+            to_blend.append(
+                MixedMissingSection(maxsec=missing, individual=True, value=0, random=False)
+            )
+    if lost:
+        if is_train:
+            to_blend.append(Blend([
+                LostSection(1),
+                LostPlusMissing(value=0, random=random),
+                LostPlusMissing(value=0, random=False)
+            ]))
+    augs.append(Blend(to_blend))
+
+    # Out-of-focus
+    if blur > 0:
+        augs.append(MixedBlurrySection(maxsec=blur))
+
+    # Warping
+    if is_train:
+        augs.append(Warp(skip=0.3, do_twist=False, rot_max=45.0, scale_max=1.1))
+
+    # Flip & rotate
+    augs.append(FlipRotate())
+
+    # Create border
+    if border:
+        augs.append(Border(targets=border))
+
+    # Recompute connected components
+    if recompute:
+        augs.append(Label(targets=recompute))
+
+    # Section gap
+    augs.append(
+        Blend(
+            SectionGap(num_secs=3, masked=True),
+            SectionGap(num_secs=4, masked=True),
+            SectionGap(num_secs=5, masked=True),
+        )
+    )
+
+    return Compose(augs)

deepem/data/augment/cortex/aug_4nm.py

@@ -10,6 +10,8 @@ def get_augmentation(
     random=False,
     recompute=False,
     border=[],
+    section_gap=0,
+    mask_section_gap=False,
     **kwargs
 ):
     augs = list()
@@ -92,4 +94,8 @@ def get_augmentation(
     if recompute:
         augs.append(Label(targets=recompute))
 
+    # Section gap
+    if section_gap > 0:
+        augs.append(SectionGap(num_secs=section_gap, masked=mask_section_gap))
+
     return Compose(augs)

deepem/data/augment/cortex/aug_8nm.py

@@ -10,6 +10,8 @@ def get_augmentation(
     random=False,
     recompute=False,
     border=[],
+    section_gap=0,
+    mask_section_gap=False,
     **kwargs
 ):
     augs = list()
@@ -92,4 +94,8 @@ def get_augmentation(
     if recompute:
         augs.append(Label(targets=recompute))
 
+    # Section gap
+    if section_gap > 0:
+        augs.append(SectionGap(num_secs=section_gap, masked=mask_section_gap))
+
     return Compose(augs)

deepem/train/option.py

@@ -124,6 +124,8 @@ def initialize(self):
         self.parser.add_argument('--noise_min', type=float, default=0.01)
         self.parser.add_argument('--noise_max', type=float, default=0.1)
         self.parser.add_argument('--noise_per_channel', action='store_true')
+        self.parser.add_argument('--section_gap', type=int, default=0)
+        self.parser.add_argument('--mask_section_gap', action='store_true')
 
         # Tilt-series electron tomography
         self.parser.add_argument('--tilt_series', type=int, default=0)
@@ -237,7 +239,8 @@ def parse(self):
 
         # Data augmentation
         aug_keys = ['recompute', 'border', 'flip','grayscale','warping','misalign',
-                    'interp','missing','blur','box','mip','lost','random']
+                    'interp','missing','blur','box','mip','lost','random',
+                    'section_gap', 'mask_section_gap']
         opt.aug_params = {k: args[k] for k in aug_keys}
 
         # Noise