From ce0166da7351b8846db7cb8bb941da19e08f7be6 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 26 Nov 2024 06:27:10 +0100
Subject: [PATCH] RoiSet.run_exports and .get_export_product_accessors no
longer take a channel directly, but rather pull these from parameters of
individual patch products
---
model_server/base/pipelines/roiset_obmap.py | 2 +-
model_server/base/roiset.py | 39 +++++++++++----------
tests/base/test_roiset.py | 13 +++----
3 files changed, 28 insertions(+), 26 deletions(-)
diff --git a/model_server/base/pipelines/roiset_obmap.py b/model_server/base/pipelines/roiset_obmap.py
index 74380a02..3bc5e00d 100644
--- a/model_server/base/pipelines/roiset_obmap.py
+++ b/model_server/base/pipelines/roiset_obmap.py
@@ -84,7 +84,7 @@ def roiset_object_map_pipeline(
rois = RoiSet.from_object_ids(d['input'], d['labeled'], RoiSetMetaParams(**k['roi_params']))
# optionally append RoiSet products
- for ki, vi in rois.get_export_product_accessors(k['patches_channel'], RoiSetExportParams(**k['export_params'])).items():
+ for ki, vi in rois.get_export_product_accessors(RoiSetExportParams(**k['export_params'])).items():
d[ki] = vi
# optionally run an object classifier if specified
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index f7cc75f2..de34993c 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -25,16 +25,22 @@ from .process import mask_largest_object
class PatchParams(BaseModel):
+ white_channel: Union[int, None] = None
+ channels: Union[List[int], None] = None
draw_bounding_box: bool = False
draw_contour: bool = False
draw_mask: bool = False
- rescale_clip: float = 0.001
- focus_metric: str = 'max_sobel'
+ rescale_clip: Union[float, None] = None
+ focus_metric: Union[str, None] = 'max_sobel'
rgb_overlay_channels: Union[List[Union[int, None]], None] = None
rgb_overlay_weights: List[float] = [1.0, 1.0, 1.0]
pad_to: Union[int, None] = 256
expanded: bool = False
+class AnnotatedPatchParams(PatchParams):
+ bounding_box_channel: int = 1
+ bounding_box_linewidth: int = 2
+
class AnnotatedZStackParams(BaseModel):
draw_label: bool = False
@@ -60,7 +66,7 @@ class RoiSetMetaParams(BaseModel):
class RoiSetExportParams(BaseModel):
patches_3d: Union[PatchParams, None] = None
- annotated_patches_2d: Union[PatchParams, None] = None
+ annotated_patches_2d: Union[AnnotatedPatchParams, None] = None
patches_2d: Union[PatchParams, None] = None
annotated_zstacks: Union[AnnotatedZStackParams, None] = None
object_classes: bool = False
@@ -704,7 +710,7 @@ class RoiSet(object):
ext = 'tif' if make_3d or patch.chroma > 3 or kwargs.get('force_tif') else 'png'
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
- if patch.dtype is np.dtype('uint16'):
+ if patch.dtype == 'uint16':
resampled = patch.apply(resample_to_8bit)
write_accessor_data_to_file(where / fname, resampled)
else:
@@ -883,11 +889,10 @@ class RoiSet(object):
"""
self._df[colname] = se
- def run_exports(self, where: Path, channel, prefix, params: RoiSetExportParams) -> dict:
+ def run_exports(self, where: Path, prefix, params: RoiSetExportParams) -> dict:
"""
Export various representations of ROIs, e.g. patches, annotated stacks, and object maps.
:param where: path of directory in which to write all export products
- :param channel: color channel of products to export
:param prefix: prefix of the name of each product's file or subfolder
:param params: RoiSetExportParams object describing which products to export and with which parameters
:return: nested dict of Path objects describing the location of export products
@@ -904,18 +909,17 @@ class RoiSet(object):
continue
if k == 'patches_3d':
df_exp = self.export_patches(
- subdir, white_channel=channel, prefix=pr, make_3d=True, **kp
+ subdir, prefix=pr, make_3d=True, **kp
)
record[k] = [str(Path(k) / fn) for fn in df_exp.patch_path]
if k == 'annotated_patches_2d':
df_exp = self.export_patches(
- subdir, prefix=pr, make_3d=False, white_channel=channel,
- bounding_box_channel=1, bounding_box_linewidth=2, **kp,
+ subdir, prefix=pr, make_3d=False, **kp,
)
record[k] = [str(Path(k) / fn) for fn in df_exp.patch_path]
if k == 'patches_2d':
df_exp = self.export_patches(
- subdir, white_channel=channel, prefix=pr, make_3d=False, **kp
+ subdir, prefix=pr, make_3d=False, **kp
)
self._df = self._df.join(df_exp.patch_path.apply(lambda x: str(Path('patches_2d') / x)))
self._df['patch_id'] = self._df.apply(lambda _: uuid4(), axis=1)
@@ -940,10 +944,9 @@ class RoiSet(object):
return record
- def get_export_product_accessors(self, channel, params: RoiSetExportParams) -> dict:
+ def get_export_product_accessors(self, params: RoiSetExportParams) -> dict:
"""
Return various representations of ROIs, e.g. patches, annotated stacks, and object maps, as accessors
- :param channel: color channel of products to export
:param params: RoiSetExportParams object describing which products to export and with which parameters
:return: ordered dict of accessors containing the specified products
"""
@@ -955,14 +958,13 @@ class RoiSet(object):
if kp is None:
continue
if k == 'patches_3d':
- interm[k] = self.get_patches_acc([channel], make_3d=True, **kp)
+ interm[k] = self.get_patches_acc(make_3d=True, **kp)
if k == 'annotated_patches_2d':
interm[k] = self.get_patches_acc(
- make_3d=False, white_channel=channel,
- bounding_box_channel=1, bounding_box_linewidth=2, **kp
+ make_3d=False, **kp
)
if k == 'patches_2d':
- interm[k] = self.get_patches_acc(make_3d=False, white_channel=channel, **kp)
+ interm[k] = self.get_patches_acc(make_3d=False, **kp)
if k == 'annotated_zstacks':
interm[k] = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kp))
if k == 'object_classes':
@@ -1147,16 +1149,15 @@ class RoiSetWithDerivedChannels(RoiSet):
)[-1]
self._df.loc[roi.Index, 'classify_by_' + name] = oc
- def run_exports(self, where: Path, channel, prefix, params: RoiSetWithDerivedChannelsExportParams) -> dict:
+ def run_exports(self, where: Path, prefix, params: RoiSetWithDerivedChannelsExportParams) -> dict:
"""
Export various representations of ROIs, e.g. patches, annotated stacks, and object maps.
:param where: path of directory in which to write all export products
- :param channel: color channel of products to export
:param prefix: prefix of the name of each product's file or subfolder
:param params: RoiSetExportParams object describing which products to export and with which parameters
:return: nested dict of Path objects describing the location of export products
"""
- record = super().run_exports(where, channel, prefix, params)
+ record = super().run_exports(where, prefix, params)
k = 'derived_channels'
if k in params.dict().keys():
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index ee73aa4b..1d4742fc 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -221,7 +221,6 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_export_object_classes(self):
record = self.test_classify_by().run_exports(
output_path / 'object_class_maps',
- 0,
'obmap',
RoiSetExportParams(object_classes=True)
)
@@ -400,12 +399,14 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
p = RoiSetExportParams(**{
'patches_3d': {},
'annotated_patches_2d': {
+ 'white_channel': 3,
'draw_bounding_box': True,
'rgb_overlay_channels': [3, None, None],
'rgb_overlay_weights': [0.2, 1.0, 1.0],
'pad_to': 512,
},
'patches_2d': {
+ 'white_channel': 3,
'draw_bounding_box': False,
'draw_mask': False,
},
@@ -420,7 +421,6 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
where = output_path / 'run_exports'
res = self.roiset.run_exports(
where,
- channel=3,
prefix='test',
params=p
)
@@ -446,21 +446,22 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
p = RoiSetExportParams(**{
'patches_3d': None,
'annotated_patches_2d': {
+ 'white_channel': 3,
'draw_bounding_box': True,
'rgb_overlay_channels': [3, None, None],
'rgb_overlay_weights': [0.2, 1.0, 1.0],
'pad_to': 512,
},
'patches_2d': {
+ 'white_channel': 3,
'draw_bounding_box': False,
'draw_mask': False,
},
'annotated_zstacks': {},
'object_classes': True,
})
- self.roiset.classify_by('dummy_class', [0], DummyInstanceMaskSegmentationModel())
+ self.roiset.classify_by('dummy_class', [3], DummyInstanceMaskSegmentationModel())
interm = self.roiset.get_export_product_accessors(
- channel=3,
params=p
)
self.assertNotIn('patches_3d', interm.keys())
@@ -485,6 +486,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
def test_run_export_expanded_2d_patch(self):
p = RoiSetExportParams(**{
'patches_2d': {
+ 'white_channel': -1,
'draw_bounding_box': False,
'draw_mask': False,
'expanded': True,
@@ -497,7 +499,6 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
where = output_path / 'run_exports_expanded_2d_patch'
res = self.roiset.run_exports(
where,
- channel=-1,
prefix='test',
params=p
)
@@ -512,6 +513,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
def test_run_export_mono_2d_patch(self):
p = RoiSetExportParams(**{
'patches_2d': {
+ 'white_channel': -1,
'draw_bounding_box': False,
'draw_mask': False,
'expanded': True,
@@ -525,7 +527,6 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
where = output_path / 'run_exports_mono_2d_patch'
res = self.roiset.run_exports(
where,
- channel=-1,
prefix='test',
params=p
)
--
GitLab