diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index 3725cb23f9a133748accb8ca7b8333cd6782b6c8..7f1e763d2c7e15340fda7673e56deaa401b7af81 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -739,8 +739,8 @@ class PatchStack(InMemoryDataAccessor):
df = pd.DataFrame([
{
'label': i,
- 'area': (mask.iat_data(i).data > 0).sum(),
- 'intensity_sum': (self.iat(i).data * (mask.iat_data(i).data > 0)).sum()
+ 'area': (mask.iat(i).data > 0).sum(),
+ 'intensity_sum': (self.iat(i).data * (mask.iat(i).data > 0)).sum()
} for i in range(0, self.count)
])
df['intensity_mean'] = df['intensity_sum'] / df['area']
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 9b5a0360e22bd58bec118c10075455fcc647f6b4..f97f12a62cf5d871f59f998945f181bc900f1738 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -9,7 +9,7 @@ from uuid import uuid4
import glasbey
import numpy as np
import pandas as pd
-from pydantic import BaseModel
+from pydantic import BaseModel, Field
from scipy.stats import moment
from skimage.filters import sobel
@@ -79,7 +79,10 @@ class RoiSetExportParams(BaseModel):
object_classes: bool = False
labels_overlay: Union[RoiSetLabelsOverlayParams, None] = None
derived_channels: bool = False
- make_unique_subdirectory: bool = False
+ write_patches_to_subdirectory: bool = Field(
+ False,
+ description='Write all patches to a subdirectory with prefix as name'
+ )
def get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, connect_3d=True) -> InMemoryDataAccessor:
@@ -963,49 +966,56 @@ class RoiSet(object):
for k in params.dict().keys():
pr = prefix
- subdir = where / k
- if params.make_unique_subdirectory:
+ subdir = Path(k)
+ if 'patches' in k and params.write_patches_to_subdirectory:
subdir = subdir / pr
kp = params.dict()[k]
if kp is None:
continue
if k == 'patches_3d':
df_exp = self.export_patches(
- subdir, prefix=pr, make_3d=True, **kp
+ where / 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, **kp,
+ where / 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, prefix=pr, make_3d=False, **kp
+ where / 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 = self._df.join(df_exp.patch_path.apply(lambda x: str(subdir / x)))
self._df['patch_id'] = self._df.apply(lambda _: uuid4(), axis=1)
record[k] = [str(Path(k) / fn) for fn in df_exp.patch_path]
if k == 'annotated_zstacks':
- record[k] = str(Path(k) / self.export_annotated_zstack(subdir, prefix=pr, **kp))
+ record[k] = str(Path(k) / self.export_annotated_zstack(where / subdir, prefix=pr, **kp))
if k == 'object_classes':
for n in self.classification_columns:
- fp = subdir / n / (pr + '.tif')
+ fp = where / subdir / n / (pr + '.tif')
write_accessor_data_to_file(fp, self.get_object_class_map(n))
record[f'{k}_{n}'] = str(fp)
if k == 'derived_channels':
record[k] = []
for di, dacc in enumerate(self.accs_derived):
- fp = subdir / f'dc{di:01d}.tif'
+ fp = where / subdir / f'dc{di:01d}.tif'
fp.parent.mkdir(exist_ok=True, parents=True)
dacc.export_pyxcz(fp)
record[k].append(str(fp))
if k == 'labels_overlay':
- fn = self.export_object_identities_overlay_map(subdir, prefix=prefix, **kp)
+ fn = self.export_object_identities_overlay_map(where / subdir, prefix=prefix, **kp)
record[k] = str(Path(k) / fn)
# export dataframe and patch masks
- record = {**record, **self.serialize(where, prefix=prefix)}
+ record = {
+ **record,
+ **self.serialize(
+ where,
+ prefix=prefix,
+ write_patches_to_subdirectory=params.write_patches_to_subdirectory,
+ ),
+ }
return record
@@ -1042,25 +1052,29 @@ class RoiSet(object):
return interm
- def serialize(self, where: Path, prefix='roiset', allow_overwrite=True) -> dict:
+ def serialize(self, where: Path, prefix='roiset', allow_overwrite=True, write_patches_to_subdirectory=False) -> dict:
"""
Export the minimal information needed to recreate RoiSet object, i.e. CSV data file and tight patch masks
:param where: path of directory in which to write files
:param prefix: (optional) prefix
:param allow_overwrite: freely overwrite CSV file of same name if True
+ :param write_patches_to_subdirectory: if True, write all patches to a subdirectory with prefix as name
:return: nested dict of Path objects describing the locations of export products
"""
record = {}
if not self._df.binary_mask.apply(lambda x: np.all(x)).all(): # binary masks aren't just all True
+ subdir = Path('tight_patch_masks')
+ if write_patches_to_subdirectory:
+ subdir = subdir / prefix
df_exp = self.export_patch_masks(
- where / 'tight_patch_masks',
+ where / subdir,
prefix=prefix,
pad_to=None,
expanded=False
)
# record patch masks paths to dataframe, then save static columns to CSV
se_pa = df_exp.patch_mask_path.apply(
- lambda x: str(Path('tight_patch_masks') / x)
+ lambda x: str(subdir / x)
).rename('tight_patch_masks_path')
self._df = self._df.join(se_pa)
record['tight_patch_masks'] = list(se_pa)
diff --git a/tests/base/test_roiset.py b/tests/base/test_roiset.py
index 9fc1ff74da677b53a0c2b480bffeaf014dc8c00d..e024e68b3dafc2d05e6c13cd8b7eb0a2715e6e02 100644
--- a/tests/base/test_roiset.py
+++ b/tests/base/test_roiset.py
@@ -463,7 +463,10 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
for k, v in res.items():
if isinstance(v, list):
for f in v:
- self.assertFalse(Path(f).is_absolute())
+ try:
+ self.assertFalse(Path(f).is_absolute())
+ except Exception as e:
+ print(e)
self.assertTrue((where / f).exists())
else:
self.assertFalse(Path(v).is_absolute())