From 0d0a86bf7f6aa27913ae20384c40f327cd1f2f3b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Tue, 2 Apr 2024 18:49:30 +0200
Subject: [PATCH] Force export of dataset and patches; just need to override
bounding box expansion
---
model_server/base/roiset.py | 24 ++++++++++--------
tests/test_roiset.py | 50 +++++++++++++++++++++++++------------
2 files changed, 47 insertions(+), 27 deletions(-)
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 29a897df..a5aaf763 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -56,11 +56,8 @@ class RoiSetExportParams(BaseModel):
patches_3d: Union[PatchParams, None] = None
annotated_patches_2d: Union[PatchParams, None] = None
patches_2d: Union[PatchParams, None] = None
- patch_masks: Union[PatchParams, None] = None
annotated_zstacks: Union[AnnotatedZStackParams, None] = None
object_classes: bool = False
- dataframe: bool = False
-
@@ -350,7 +347,13 @@ class RoiSet(object):
om[self.acc_obj_ids.data == roi.label] = oc
self.object_class_maps[name] = InMemoryDataAccessor(om)
- def export_patch_masks(self, where: Path, pad_to: int = 256, prefix='mask', **kwargs) -> list:
+ def export_dataframe(self, csv_path: Path):
+ csv_path.parent.mkdir(parents=True, exist_ok=True)
+ self._df.drop(['slice', 'relative_slice', 'mask'], axis=1).to_csv(csv_path, index=False)
+ return csv_path
+
+
+ def export_patch_masks(self, where: Path, pad_to: int = 256, prefix='mask') -> list:
patches_acc = self.get_patch_masks(pad_to=pad_to)
exported = []
@@ -538,6 +541,11 @@ class RoiSet(object):
if not self.count:
return
raw_ch = self.acc_raw.get_one_channel_data(channel)
+
+ # export dataframe and patch masks
+ record['dataframe'] = self.export_dataframe(where / 'dataframe' / (prefix + '.csv'))
+ self.export_patch_masks(where / 'patch_masks', prefix=prefix, pad_to=None)
+
for k in params.dict().keys():
subdir = where / k
pr = prefix
@@ -560,8 +568,6 @@ class RoiSet(object):
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['patch_id'] = self._df.apply(lambda _: uuid4(), axis=1)
- if k == 'patch_masks':
- self.export_patch_masks(subdir, prefix=pr, **kp)
if k == 'annotated_zstacks':
self.export_annotated_zstack(subdir, prefix=pr, **kp)
if k == 'object_classes':
@@ -569,11 +575,7 @@ class RoiSet(object):
fp = subdir / kc / (pr + '.tif')
write_accessor_data_to_file(fp, acc)
record[f'{k}_{kc}'] = fp
- if k == 'dataframe':
- dfpa = subdir / (pr + '.csv')
- dfpa.parent.mkdir(parents=True, exist_ok=True)
- self._df.drop(['slice', 'relative_slice', 'mask'], axis=1).to_csv(dfpa, index=False)
- record[k] = dfpa
+
return record
diff --git a/tests/test_roiset.py b/tests/test_roiset.py
index 596b66d0..b5e9175a 100644
--- a/tests/test_roiset.py
+++ b/tests/test_roiset.py
@@ -1,3 +1,5 @@
+import os
+import re
import unittest
import numpy as np
@@ -333,21 +335,37 @@ class TestRoiSetFromZmask(unittest.TestCase):
df_test = pd.read_csv(where_df)
- # zmask = np.zeros((*self.stack.hw, 1, self.stack.nz), dtype=bool)
- print('hi')
-
- fn = output_path / 'roiset_from_3d' / 'patch_masks' / 'ref-la{:04d}-zi{:04d}.png'
- patch_masks = {}
-
- def _label_obj(r):
- sl = np.s_[r.ebb_y0:r.ebb_y1, r.ebb_x0:r.ebb_x1, :, r.zi:r.zi + 1]
- self.assertEqual(str(sl), r.slice)
- patch_masks[r.label] = generate_file_accessor(str(fn).format(r.label, r.zi)).data
- # zmask[sl] = True
-
- df_test.apply(lambda x: _label_obj(x), axis=1)
-
- roiset_test = RoiSet.from_df_and_patch_masks(self.stack, df_test, patch_masks)
- print('')
+ # check that patches are correct size
+ where_patch_masks = output_path / 'roiset_from_3d' / 'patch_masks'
+ for pmf in where_patch_masks.iterdir():
+ self.assertTrue(pmf.suffix.upper() == '.PNG')
+ la = int(re.search(r'la([\d]+)', str(pmf)).group(1))
+ roi_q = df_test.loc[df_test.label == la, :]
+ self.assertEqual(len(roi_q), 1)
+ roi = roi_q.iloc[0]
+ h = int(roi.y1 - roi.y0)
+ w = int(roi.x1 - roi.x0)
+ m_acc = generate_file_accessor(pmf)
+ self.assertEqual((h, w), m_acc.hw)
+
+
+ # df_test = pd.read_csv(where_df)
+ #
+ # # zmask = np.zeros((*self.stack.hw, 1, self.stack.nz), dtype=bool)
+ # print('hi')
+ #
+ # fn = output_path / 'roiset_from_3d' / 'patch_masks' / 'ref-la{:04d}-zi{:04d}.png'
+ # patch_masks = {}
+ #
+ # def _label_obj(r):
+ # sl = np.s_[r.ebb_y0:r.ebb_y1, r.ebb_x0:r.ebb_x1, :, r.zi:r.zi + 1]
+ # self.assertEqual(str(sl), r.slice)
+ # patch_masks[r.label] = generate_file_accessor(str(fn).format(r.label, r.zi)).data
+ # # zmask[sl] = True
+ #
+ # df_test.apply(lambda x: _label_obj(x), axis=1)
+ #
+ # roiset_test = RoiSet.from_df_and_patch_masks(self.stack, df_test, patch_masks)
+ # print('')
--
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