diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index fec80c819ad808a1f8ca2afa09b6b0fd65a8b4fe..4b91eb5cda12dc79c3b1bd300c5630d1370d2c91 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -3,12 +3,12 @@ import os
from pathlib import Path
import numpy as np
-from skimage.io import imread
+from skimage.io import imread, imsave
import czifile
import tifffile
-from extensions.chaeo.accessors import InvalidDataForPatchStackError
+from base.process import make_rgb
from model_server.base.process import is_mask
class GenericImageDataAccessor(ABC):
@@ -184,33 +184,49 @@ class CziImageFileAccessor(GenericImageFileAccessor):
return sc
-def write_accessor_data_to_file(fpath: Path, accessor: GenericImageDataAccessor, mkdir=True) -> bool:
+def write_accessor_data_to_file(fpath: Path, acc: GenericImageDataAccessor, mkdir=True) -> bool:
"""
Export an image accessor to file.
:param fpath: complete path including filename and extension
- :param accessor: image accessor to be written
+ :param acc: image accessor to be written
:param mkdir: create any needed subdirectories in fpath if True
:return: True
"""
+ if 'P' in acc.shape_dict.keys():
+ raise FileWriteError(f'Can only write single-position accessor to file')
+ ext = fpath.suffix.upper()
if mkdir:
fpath.parent.mkdir(parents=True, exist_ok=True)
- try:
+
+ if ext == '.PNG':
+ if acc.dtype != 'uint8':
+ raise FileWriteError(f'Invalid data type {acc.dtype}')
+ if acc.chroma == 1:
+ data = acc.data[:, :, 0, 0]
+ elif acc.chroma == 2: # add a blank blue channel
+ data = make_rgb(acc.data)
+ else: # preserve RGB order
+ data = acc.data[:, :, :, 0]
+ imsave(fpath, data, check_contrast=False)
+ return True
+
+ elif ext in ['.TIF', '.TIFF']:
zcyx= np.moveaxis(
- accessor.data, # yxcz
+ acc.data, # yxcz
[3, 2, 0, 1],
[0, 1, 2, 3]
)
- if accessor.is_mask():
- if accessor.dtype == 'bool':
+ if acc.is_mask():
+ if acc.dtype == 'bool':
data = (zcyx * 255).astype('uint8')
else:
data = zcyx.astype('uint8')
tifffile.imwrite(fpath, data, imagej=True)
else:
tifffile.imwrite(fpath, zcyx, imagej=True)
- except:
- raise FileWriteError(f'Unable to write data to file')
+ else:
+ raise FileWriteError(f'Unable to write data to file of extension {ext}')
return True
@@ -256,7 +272,7 @@ class PatchStack(InMemoryDataAccessor):
self._data = nda
def iat(self, i):
- return self.data[i, :, :, :, :]
+ return InMemoryDataAccessor(self.data[i, :, :, :, :])
def iat_yxcz(self, i):
return self.iat(i)
@@ -307,6 +323,7 @@ def make_patch_stack_from_file(fpath): # interpret z-dimension as patch positio
return PatchStack(pyxcz)
+
class Error(Exception):
pass
@@ -328,5 +345,8 @@ class InvalidAxisKey(Error):
class InvalidDataShape(Error):
pass
+class InvalidDataForPatchStackError(Error):
+ pass
+
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 819f8552660f1051f2bf3e713faf74d21e58d508..a66f97414c61b163403abfb75d96c119f616400b 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -17,7 +17,6 @@ from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAc
from model_server.base.models import InstanceSegmentationModel
from model_server.base.process import pad, rescale, resample_to_8bit, make_rgb
from base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
-from model_server.extensions.chaeo.accessors import write_patch_to_file
from base.accessors import PatchStack
from base.process import mask_largest_object
@@ -294,7 +293,7 @@ class RoiSet(object):
for i, roi in enumerate(self):
oc = np.unique(
mask_largest_object(
- obmap_patches.iat(i)
+ obmap_patches.iat(i).data
)
)[1]
self._df.loc[roi.Index, 'classify_by_' + name] = oc
@@ -309,7 +308,7 @@ class RoiSet(object):
patch = patches_acc.iat_yxcz(i)
ext = 'png'
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
- write_patch_to_file(where, fname, patch)
+ write_accessor_data_to_file(where / fname, patch)
exported.append(fname)
return exported
@@ -324,9 +323,10 @@ class RoiSet(object):
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
if patch.dtype is np.dtype('uint16'):
- write_patch_to_file(where, fname, resample_to_8bit(patch.data))
+ resampled = InMemoryDataAccessor(resample_to_8bit(patch.data))
+ write_accessor_data_to_file(where / fname, resampled)
else:
- write_patch_to_file(where, fname, patch)
+ write_accessor_data_to_file(where / fname, patch)
exported.append({
'df_index': roi.Index,
diff --git a/model_server/extensions/chaeo/accessors.py b/model_server/extensions/chaeo/accessors.py
deleted file mode 100644
index 7c9f74e57caf5413e515e89eff49622967cd4c2c..0000000000000000000000000000000000000000
--- a/model_server/extensions/chaeo/accessors.py
+++ /dev/null
@@ -1,41 +0,0 @@
-import numpy as np
-from skimage.io import imsave
-from tifffile import imwrite
-
-from base.process import make_rgb
-
-
-# TODO: move this as method in base.accessors
-def write_patch_to_file(where, fname, yxcz):
- ext = fname.split('.')[-1].upper()
- where.mkdir(parents=True, exist_ok=True)
-
- if ext == 'PNG':
- assert yxcz.dtype == 'uint8', f'Invalid data type {yxcz.dtype}'
- assert yxcz.shape[2] <= 3, f'Cannot export images with more than 3 channels as PNGs'
- assert yxcz.shape[3] == 1, f'Cannot export z-stacks as PNGs'
- if yxcz.shape[2] == 1:
- outdata = yxcz[:, :, 0, 0]
- elif yxcz.shape[2] == 2: # add a blank blue channel
- outdata = make_rgb(yxcz)
- else: # preserve RGB order
- outdata = yxcz[:, :, :, 0]
- imsave(where / fname, outdata, check_contrast=False)
- return True
-
- elif ext in ['TIF', 'TIFF']:
- zcyx = np.moveaxis(yxcz, [3, 2, 0, 1], [0, 1, 2, 3])
- imwrite(where / fname, zcyx, imagej=True)
- return True
-
- else:
- raise Exception(f'Unsupported file extension: {ext}')
-
-
-class Error(Exception):
- pass
-
-class InvalidDataForPatchStackError(Error):
- pass
-
-
diff --git a/model_server/extensions/chaeo/batch_jobs/coloring_book.py b/model_server/extensions/chaeo/batch_jobs/coloring_book.py
index a3a9c5268a12cac204897d9ecd5dba4d8a648ad6..e65dd1d27345852d2687715de5d91cfd90f770b9 100644
--- a/model_server/extensions/chaeo/batch_jobs/coloring_book.py
+++ b/model_server/extensions/chaeo/batch_jobs/coloring_book.py
@@ -7,7 +7,7 @@ from skimage.measure import label, regionprops_table
import tifffile
-from model_server.extensions.chaeo.accessors import MonoPatchStack
+from model_server.base.accessors import PatchStack
from model_server.extensions.ilastik.models import IlastikPixelClassifierModel
from model_server.base.accessors import write_accessor_data_to_file, InMemoryDataAccessor
@@ -19,7 +19,7 @@ if __name__ == '__main__':
min_area = 400
tf = tifffile.imread(root / '20231008-162336-z04-TL.tif')
- instack = MonoPatchStack(np.moveaxis(tf, 0, -1))
+ instack = PatchStack(np.moveaxis(tf, 0, -1))
px_mod = IlastikPixelClassifierModel(params={'project_file': px_ilp})
pxmaps = []
diff --git a/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py b/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
index 5d9625b55b03cc25a8c9476d6ac27af166de38dd..04e0c20e31d2da78ab11bec16908333e56a7c74f 100644
--- a/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/model_server/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -3,7 +3,7 @@ import numpy as np
import pandas as pd
import skimage
-from model_server.extensions.chaeo.accessors import MonoPatchStackFromFile
+from model_server.base.accessors import make_patch_stack_from_file
from model_server.extensions.chaeo.models import generate_ilastik_object_classifier
from extensions.ilastik.models import PatchStackObjectClassifier
from model_server.base.accessors import GenericImageDataAccessor, write_accessor_data_to_file
@@ -69,9 +69,9 @@ if __name__ == '__main__':
classifier_file = generate_ilastik_object_classifier(
template_ilp,
root / 'new_auto_obj.ilp',
- MonoPatchStackFromFile(root / 'zstack_train_raw.tif'),
- MonoPatchStackFromFile(root / 'zstack_train_mask.tif'),
- MonoPatchStackFromFile(root / 'zstack_train_label.tif'),
+ make_patch_stack_from_file(root / 'zstack_train_raw.tif'),
+ make_patch_stack_from_file(root / 'zstack_train_mask.tif'),
+ make_patch_stack_from_file(root / 'zstack_train_label.tif'),
label_names,
allow_multiple_objects=False
)
@@ -81,17 +81,17 @@ if __name__ == '__main__':
infer_and_compare(
classifier,
'train',
- MonoPatchStackFromFile(root / 'zstack_train_raw.tif'),
- MonoPatchStackFromFile(root / 'zstack_train_mask.tif'),
- MonoPatchStackFromFile(root / 'zstack_train_label.tif')
+ make_patch_stack_from_file(root / 'zstack_train_raw.tif'),
+ make_patch_stack_from_file(root / 'zstack_train_mask.tif'),
+ make_patch_stack_from_file(root / 'zstack_train_label.tif')
)
# run test set
infer_and_compare(
classifier,
'test',
- MonoPatchStackFromFile(root / 'zstack_test_raw.tif'),
- MonoPatchStackFromFile(root / 'zstack_test_mask.tif'),
- MonoPatchStackFromFile(root / 'zstack_test_label.tif'),
+ make_patch_stack_from_file(root / 'zstack_test_raw.tif'),
+ make_patch_stack_from_file(root / 'zstack_test_mask.tif'),
+ make_patch_stack_from_file(root / 'zstack_test_label.tif'),
)
diff --git a/model_server/extensions/chaeo/models.py b/model_server/extensions/chaeo/models.py
index 58235d81ed8d56845d220cd6203b7ed22ec6624c..865537e67ba79738a82e5b7e63472210026657f2 100644
--- a/model_server/extensions/chaeo/models.py
+++ b/model_server/extensions/chaeo/models.py
@@ -5,7 +5,7 @@ import h5py
import numpy as np
import skimage
-from model_server.extensions.chaeo.accessors import PatchStack
+from model_server.base.accessors import PatchStack
def generate_ilastik_object_classifier(
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index 5f765ba709eb30364eda1e2c9fa60db57f5c0f69..89fe2b98d1f8ea25702e8a221c6178e8fe3a645b 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -295,6 +295,6 @@ class TestIlastikObjectClassification(unittest.TestCase):
res_patches, _ = self.object_classifier.infer(raw_patches, patch_masks)
self.assertEqual(res_patches.count, self.roiset.count)
for pi in range(0, res_patches.count): # assert that there is only one nonzero label per patch
- unique = np.unique(res_patches.iat(pi))
+ unique = np.unique(res_patches.iat(pi).data)
self.assertEqual(len(unique), 2)
self.assertEqual(unique[0], 0)