diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 943aedf2cc205c7fca6d6305ad52f3484b1f4515..403ea765a5faf8cd4511f5207c3f451c8dca836d 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -257,18 +257,18 @@ class RoiSet(object):
projected = self.acc_raw.data.max(axis=-1)
return projected
- def get_patches_acc(self, channel=None, **kwargs): # padded, un-annotated 2d patches
+ def get_patches_acc(self, channel=None, **kwargs) -> PatchStack: # padded, un-annotated 2d patches
if channel:
patches_df = self.get_patches(white_channel=channel, **kwargs)
else:
patches_df = self.get_patches(**kwargs)
return PatchStack(list(patches_df.patch))
- def export_annotated_zstack(self, where, prefix='zstack', **kwargs) -> Path:
+ def export_annotated_zstack(self, where, prefix='zstack', **kwargs) -> str(Path):
annotated = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kwargs))
fp = where / (prefix + '.tif')
write_accessor_data_to_file(fp, annotated)
- return fp
+ return str(fp)
def get_zmask(self, mask_type='boxes'):
"""
@@ -337,24 +337,22 @@ class RoiSet(object):
def export_patch_masks(self, where: Path, pad_to: int = None, prefix='mask', expanded=False) -> list:
- patches_df = self.get_patch_masks(pad_to=pad_to, expanded=expanded)
+ patches_df = self.get_patch_masks(pad_to=pad_to, expanded=expanded).copy()
- exported = []
def _export_patch_mask(roi):
patch = InMemoryDataAccessor(roi.patch_mask)
ext = 'png'
fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
write_accessor_data_to_file(where / fname, patch)
- exported.append(fname)
+ return str(where / fname)
- for roi in patches_df.itertuples(): # just used for label info
- _export_patch_mask(roi)
- return exported
+ patches_df['patch_mask_path'] = patches_df.apply(_export_patch_mask, axis=1)
+ return patches_df
- def export_patches(self, where: Path, prefix='patch', **kwargs) -> list:
+ def export_patches(self, where: Path, prefix='patch', **kwargs) -> pd.DataFrame:
make_3d = kwargs.get('make_3d', False)
- patches_df = self.get_patches(**kwargs)
+ patches_df = self.get_patches(**kwargs).copy()
def _export_patch(roi):
patch = InMemoryDataAccessor(roi.patch)
@@ -366,14 +364,10 @@ class RoiSet(object):
write_accessor_data_to_file(where / fname, resampled)
else:
write_accessor_data_to_file(where / fname, patch)
+ return str(where / fname)
- exported.append(where / fname)
-
- exported = []
- for roi in patches_df.itertuples(): # just used for label info
- _export_patch(roi)
-
- return exported
+ patches_df['patch_path'] = patches_df.apply(_export_patch, axis=1)
+ return patches_df
def get_patch_masks(self, pad_to: int = None, expanded: bool = False) -> pd.DataFrame:
def _make_patch_mask(roi):
@@ -552,29 +546,30 @@ class RoiSet(object):
if kp is None:
continue
if k == 'patches_3d':
- record[k] = self.export_patches(
+ df_exp = self.export_patches(
subdir, white_channel=channel, prefix=pr, make_3d=True, expanded=True, **kp
)
+ record[k] = list(df_exp.patch_path)
if k == 'annotated_patches_2d':
- record[k] = self.export_patches(
+ df_exp = self.export_patches(
subdir, prefix=pr, make_3d=False, white_channel=channel,
bounding_box_channel=1, bounding_box_linewidth=2, **kp,
)
+ record[k] = list(df_exp.patch_path)
if k == 'patches_2d':
- files = self.export_patches(
+ df_exp = self.export_patches(
subdir, white_channel=channel, prefix=pr, make_3d=False, **kp
)
- df_patches = pd.DataFrame(files)
- self._df = pd.merge(self._df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
+ self._df = self._df.join(df_exp.patch_path)
self._df['patch_id'] = self._df.apply(lambda _: uuid4(), axis=1)
- record[k] = files
+ record[k] = list(df_exp.patch_path)
if k == 'annotated_zstacks':
record[k] = self.export_annotated_zstack(subdir, prefix=pr, **kp)
if k == 'object_classes':
for kc, acc in self.object_class_maps.items():
fp = subdir / kc / (pr + '.tif')
write_accessor_data_to_file(fp, acc)
- record[f'{k}_{kc}'] = fp
+ record[f'{k}_{kc}'] = str(fp)
return record
@@ -586,13 +581,15 @@ class RoiSet(object):
:return: nested dict of Path objects describing the locations of export products
"""
record = {}
- record['dataframe'] = self.export_dataframe(where / 'dataframe' / (prefix + '.csv'))
- record['tight_patch_masks'] = self.export_patch_masks(
+ df_exp = self.export_patch_masks(
where / 'tight_patch_masks',
prefix=prefix,
pad_to=None,
expanded=False
)
+ self._df = self._df.join(df_exp.patch_mask_path)
+ record['dataframe'] = str(self.export_dataframe(where / 'dataframe' / (prefix + '.csv')))
+ record['tight_patch_masks'] = list(df_exp.patch_mask_path)
return record
@staticmethod
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index 0d507b3f90f3346335f9798a84e77efea94baf35..fad797404e8cbda6d552aba818c5c7a1c11817d6 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -102,14 +102,14 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_make_expanded_2d_patches(self):
roiset = self._make_roi_set()
- files = roiset.export_patches(
+ df_res = roiset.export_patches(
output_path / 'expanded_2d_patches',
draw_bounding_box=True,
expanded=True,
pad_to=256,
)
df = roiset.get_df()
- for f in files:
+ for f in df_res.patch_path:
acc = generate_file_accessor(f)
la = int(re.search(r'la([\d]+)', str(f)).group(1))
roi_q = df.loc[df.label == la, :]
@@ -118,13 +118,13 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_make_tight_2d_patches(self):
roiset = self._make_roi_set()
- files = roiset.export_patches(
+ df_res = roiset.export_patches(
output_path / 'tight_2d_patches',
draw_bounding_box=True,
expanded=False
)
df = roiset.get_df()
- for f in files: # all exported files are same shape as bounding boxes in RoiSet's datatable
+ for f in df_res.patch_path: # all exported files are same shape as bounding boxes in RoiSet's datatable
acc = generate_file_accessor(f)
la = int(re.search(r'la([\d]+)', str(f)).group(1))
roi_q = df.loc[df.label == la, :]
@@ -134,13 +134,13 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_make_expanded_3d_patches(self):
roiset = self._make_roi_set()
- files = roiset.export_patches(
+ df_res = roiset.export_patches(
output_path / '3d_patches',
make_3d=True,
expanded=True
)
- self.assertGreaterEqual(len(files), 1)
- for f in files:
+ self.assertGreaterEqual(len(df_res), 1)
+ for f in df_res.patch_path:
acc = generate_file_accessor(f)
self.assertGreater(acc.nz, 1)
@@ -178,10 +178,10 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
def test_make_binary_masks(self):
roiset = self._make_roi_set()
- files = roiset.export_patch_masks(output_path / '2d_mask_patches', )
+ df_res = roiset.export_patch_masks(output_path / '2d_mask_patches', )
df = roiset.get_df()
- for f in files: # all exported files are same shape as bounding boxes in RoiSet's datatable
+ for f in df_res.patch_mask_path: # all exported files are same shape as bounding boxes in RoiSet's datatable
acc = generate_file_accessor(output_path / '2d_mask_patches' / f)
la = int(re.search(r'la([\d]+)', str(f)).group(1))
roi_q = df.loc[df.label == la, :]
@@ -244,18 +244,18 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
)
def test_multichannel_to_mono_2d_patches(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'mono_2d_patches',
white_channel=3,
draw_bounding_box=True,
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 1)
def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'mono_2d_patches_rgb_bbox',
white_channel=3,
draw_bounding_box=True,
@@ -263,11 +263,11 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 3)
def test_multichannnel_to_rgb_2d_patches_bbox(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'rgb_2d_patches_bbox',
white_channel=4,
rgb_overlay_channels=(3, None, None),
@@ -278,11 +278,11 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 3)
def test_multichannnel_to_rgb_2d_patches_mask(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'rgb_2d_patches_mask',
white_channel=4,
rgb_overlay_channels=(3, None, None),
@@ -292,11 +292,11 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 3)
def test_multichannnel_to_rgb_2d_patches_contour(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'rgb_2d_patches_contour',
rgb_overlay_channels=(3, None, None),
draw_contour=True,
@@ -305,17 +305,17 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 3)
self.assertEqual(result.get_one_channel_data(2).data.max(), 0) # blue channel is black
def test_multichannel_to_multichannel_tif_patches(self):
- files = self.roiset.export_patches(
+ df_res = self.roiset.export_patches(
output_path / 'multichannel' / 'multichannel_tif_patches',
expanded=True,
pad_to=256,
)
- result = generate_file_accessor(files[0])
+ result = generate_file_accessor(df_res.patch_path.iloc[0])
self.assertEqual(result.chroma, 5)
self.assertEqual(result.nz, 1)
@@ -342,6 +342,42 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
self.assertEqual(result.nz, self.roiset.acc_raw.nz)
self.assertEqual(result.chroma, 1)
+ def test_run_exports(self):
+ p = RoiSetExportParams(**{
+ 'patches_3d': {},
+ 'annotated_patches_2d': {
+ 'draw_bounding_box': True,
+ 'rgb_overlay_channels': [3, None, None],
+ 'rgb_overlay_weights': [0.2, 1.0, 1.0],
+ 'pad_to': 512,
+ },
+ 'patches_2d': {
+ 'draw_bounding_box': False,
+ 'draw_mask': False,
+ },
+ 'patch_masks': {
+ 'pad_to': 256,
+ },
+ 'annotated_zstacks': {},
+ 'object_classes': True,
+ 'dataframe': True,
+ })
+
+ res = self.roiset.run_exports(
+ output_path / 'run_exports',
+ channel=3,
+ prefix='test',
+ params=p
+ )
+
+ for k, v in res.items():
+ if isinstance(v, list):
+ for f in v:
+ self.assertTrue(Path(f).exists())
+ else:
+ self.assertTrue(Path(v).exists())
+
+
class TestRoiSetFromZmask(unittest.TestCase):
def setUp(self) -> None: