diff --git a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
index 0d99fe5f5267d0ff6969235a4f44222ea478b5aa..1e263ddf8cb834fa0e416773a6adf6f5f6b5c234 100644
--- a/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
+++ b/extensions/chaeo/batch_jobs/20231023_Porto_4ch.py
@@ -22,19 +22,18 @@ if __name__ == '__main__':
# write single-position TIF color stacks
where_proc = Path(where_output) / 'proc'
- # for pos in range(0, cf.shape[cf.axes.index('S')]):
+
+ for pos in range(0, cf.shape[cf.axes.index('S')]):
# for pos in [0, 50, 100, 150, 200]:
- # fname = f'{czi_filepath.stem}_p{pos:02d}.tif'
- # write_accessor_data_to_file(
- # where_proc / fname,
- # get_accessor_from_multiposition_czi(cf, pos)
- # )
- # print(f'Wrote file {fname}')
+ fname = f'{czi_filepath.stem}_p{pos:04d}.tif'
+ write_accessor_data_to_file(
+ where_proc / fname,
+ get_accessor_from_multiposition_czi(cf, pos)
+ )
+ print(f'Wrote file {fname}')
px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_4ch_02.ilp').__str__()
- where_proc = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/output/batch-output-20240126-0003/proc')
-
params = {
'pxmap_threshold': 0.25,
'pxmap_foreground_channel': 0,
@@ -55,6 +54,7 @@ if __name__ == '__main__':
'rgb_overlay_channels': (1, None, None),
'rgb_overlay_weights': (0.2, 1.0, 1.0),
'draw_label_on_zstack': True,
+ 'pxmap_use_all_channels': True,
}
input_files = get_matching_files(where_proc, 'tif', coord_filter={})
@@ -66,14 +66,13 @@ if __name__ == '__main__':
[IlastikPixelClassifierModel(params={'project_file': Path(px_ilp)})],
params,
catch_and_continue=False,
- chunk_size=25,
+ chunk_size=50,
)
write_ecotaxa_tsv_chunked_subdirectories(
where_output,
'workflow_data.csv',
sample_id=sample_id,
- scope_id='EMBL-MS-Zeiss-LSM900'
+ scope_id='EMBL-MS-Zeiss-LSM900',
)
-
print('Finished')
\ No newline at end of file
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 3231ef6befc27cc21bbcb4e14d7db67c16907f79..6adf7a077395f331061754b3061a2f4a2c8af210 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -31,6 +31,7 @@ def get_zmask_meta(
zmask_clip: int = None,
zmask_filters: Dict = None,
zmask_type: str = 'boxes',
+ pxmap_use_all_channels: bool = False,
**kwargs,
) -> tuple:
ti = Timer()
@@ -41,9 +42,15 @@ def get_zmask_meta(
# MIP if no zmask z-index is given, then classify pixels
if isinstance(zmask_zindex, int):
assert 0 < zmask_zindex < stack.nz
- zmask_data = stack.get_one_channel_data(channel=segmentation_channel).data[:, :, :, zmask_zindex]
+ if pxmap_use_all_channels:
+ zmask_data = stack.data[:, :, :, zmask_zindex]
+ else:
+ zmask_data = stack.get_one_channel_data(channel=segmentation_channel).data[:, :, :, zmask_zindex]
else:
- zmask_data = stack.get_one_channel_data(channel=segmentation_channel).data.max(axis=-1, keepdims=True)
+ if pxmap_use_all_channels:
+ zmask_data = stack.data.max(axis=-1, keepdims=True)
+ else:
+ zmask_data = stack.get_one_channel_data(channel=segmentation_channel).data.max(axis=-1, keepdims=True)
if zmask_clip:
zmask_data = rescale(zmask_data, zmask_clip)
mip = InMemoryDataAccessor(
@@ -68,7 +75,8 @@ def get_zmask_meta(
ti.click('generate_zmasks')
# record pixel scale
- df['pixel_scale_in_micrometers'] = float(stack.pixel_scale_in_micrometers.get('X'))
+ px_scale = stack.pixel_scale_in_micrometers.get('X')
+ df['pixel_scale_in_micrometers'] = float(px_scale) if px_scale is not None else None
return ti, stack, fstem, obmask, pxmap, zmask, zmask_meta, df, interm
@@ -80,7 +88,7 @@ def export_patches_from_multichannel_zstack(
models: List[Model],
pxmap_threshold: float,
pxmap_foreground_channel: int,
- segmentation_channel: int,
+ segmentation_channel: int, # -1 to use all channels
patches_channel: int,
zmask_zindex: int = None, # None for MIP,
zmask_clip: int = None,
@@ -99,6 +107,7 @@ def export_patches_from_multichannel_zstack(
export_patch_masks=True,
rgb_overlay_channels=(None, None, None),
rgb_overlay_weights=(1.0, 1.0, 1.0),
+ **kwargs,
) -> Dict:
pixel_classifier = models[0]
@@ -113,6 +122,7 @@ def export_patches_from_multichannel_zstack(
zmask_expand_box_by=zmask_expand_box_by,
zmask_filters=zmask_filters,
zmask_type=zmask_type,
+ **kwargs,
)
if export_pixel_probabilities:
diff --git a/tests/test_accessors.py b/tests/test_accessors.py
deleted file mode 100644
index 557970ea691b91b228a43e29993bc4068c8d88db..0000000000000000000000000000000000000000
--- a/tests/test_accessors.py
+++ /dev/null
@@ -1,118 +0,0 @@
-import unittest
-
-import numpy as np
-
-from conf.testing import czifile, output_path, monopngfile, rgbpngfile, tifffile, monozstackmask
-from model_server.accessors import CziImageFileAccessor, DataShapeError, generate_file_accessor, InMemoryDataAccessor, PngFileAccessor, write_accessor_data_to_file, TifSingleSeriesFileAccessor
-
-class TestCziImageFileAccess(unittest.TestCase):
-
- def setUp(self) -> None:
- pass
-
- def test_tiffile_is_correct_shape(self):
- tf = generate_file_accessor(tifffile['path'])
-
- self.assertIsInstance(tf, TifSingleSeriesFileAccessor)
- self.assertEqual(tf.shape_dict['Y'], tifffile['h'])
- self.assertEqual(tf.shape_dict['X'], tifffile['w'])
- self.assertEqual(tf.chroma, tifffile['c'])
- self.assertTrue(tf.is_3d())
- self.assertEqual(len(tf.data.shape), 4)
- self.assertEqual(tf.shape[0], tifffile['h'])
- self.assertEqual(tf.shape[1], tifffile['w'])
-
- def test_czifile_is_correct_shape(self):
- cf = CziImageFileAccessor(czifile['path'])
- self.assertEqual(cf.shape_dict['Y'], czifile['h'])
- self.assertEqual(cf.shape_dict['X'], czifile['w'])
- self.assertEqual(cf.chroma, czifile['c'])
- self.assertFalse(cf.is_3d())
- self.assertEqual(len(cf.data.shape), 4)
- self.assertEqual(cf.shape[0], czifile['h'])
- self.assertEqual(cf.shape[1], czifile['w'])
-
- def test_get_single_channel_from_zstack(self):
- w = 256
- h = 512
- nc = 4
- nz = 11
- c = 3
- cf = InMemoryDataAccessor(np.random.rand(h, w, nc, nz))
- sc = cf.get_one_channel_data(c)
- self.assertEqual(sc.shape, (h, w, 1, nz))
-
- def test_write_single_channel_tif(self):
- ch = 4
- cf = CziImageFileAccessor(czifile['path'])
- mono = cf.get_one_channel_data(ch)
- self.assertTrue(
- write_accessor_data_to_file(
- output_path / f'{cf.fpath.stem}_ch{ch}.tif',
- mono
- )
- )
- self.assertEqual(cf.data.shape[0:2], mono.data.shape[0:2])
- self.assertEqual(cf.data.shape[3], mono.data.shape[2])
-
- def test_conform_data_shorter_than_xycz(self):
- h = 256
- w = 512
- data = np.random.rand(h, w, 1)
- acc = InMemoryDataAccessor(data)
- self.assertEqual(
- InMemoryDataAccessor.conform_data(data).shape,
- (256, 512, 1, 1)
- )
- self.assertEqual(
- acc.shape_dict,
- {'Y': 256, 'X': 512, 'C': 1, 'Z': 1}
- )
-
- def test_conform_data_longer_than_xycz(self):
- data = np.random.rand(256, 512, 12, 8, 3)
- with self.assertRaises(DataShapeError):
- acc = InMemoryDataAccessor(data)
-
-
- def test_write_multichannel_image_preserve_axes(self):
- h = 256
- w = 512
- c = 3
- nz = 10
-
- yxcz = (2**8 * np.random.rand(h, w, c, nz)).astype('uint8')
- acc = InMemoryDataAccessor(yxcz)
- fp = output_path / f'rand3d.tif'
- self.assertTrue(
- write_accessor_data_to_file(fp, acc)
- )
- # need to sort out x,y flipping since np convention yxcz flips axes in 3d tif
- self.assertEqual(acc.shape_dict['X'], w, acc.shape_dict)
- self.assertEqual(acc.shape_dict['Y'], h, acc.shape_dict)
-
- # re-open file and check axes order
- from tifffile import TiffFile
- fh = TiffFile(fp)
- self.assertEqual(len(fh.series), 1)
- se = fh.series[0]
- fh_shape_dict = {se.axes[i]: se.shape[i] for i in range(0, len(se.shape))}
- self.assertEqual(fh_shape_dict, acc.shape_dict, 'Axes are not preserved in TIF output')
-
- def test_read_png(self, pngfile=rgbpngfile):
- acc = PngFileAccessor(pngfile['path'])
- self.assertEqual(acc.hw, (pngfile['h'], pngfile['w']))
- self.assertEqual(acc.chroma, pngfile['c'])
- self.assertEqual(acc.nz, 1)
-
- def test_read_mono_png(self):
- return self.test_read_png(pngfile=monopngfile)
-
- def test_read_zstack_mono_mask(self):
- acc = generate_file_accessor(monozstackmask['path'])
- self.assertTrue(acc.is_mask())
-
- def test_read_in_pixel_scale_from_czi(self):
- cf = CziImageFileAccessor(czifile['path'])
- pxs = cf.pixel_scale_in_micrometers
- self.assertAlmostEqual(pxs['X'], czifile['um_per_pixel'], places=3)
\ No newline at end of file