From cb8000e30e412780883b8d85c5817dab72a2710f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 13:20:01 +0100
Subject: [PATCH] Propagate filename to export products
---
extensions/chaeo/workflows.py | 14 +++++++-------
extensions/chaeo/zmask.py | 15 ++++++++-------
2 files changed, 15 insertions(+), 14 deletions(-)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 5e13b819..9171aaa0 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -58,12 +58,12 @@ def infer_object_map_from_zstack(
pxmap, _ = pixel_classifier.infer(mip)
ti.click('infer_pixel_probability')
- if exports.pixel_probabilities:
- write_accessor_data_to_file(
- Path(output_folder_path) / 'pixel_probabilities' / (fstem + '.tif'),
- pxmap
- )
- ti.click('export_pixel_probability')
+ # if exports.pixel_probabilities:
+ # write_accessor_data_to_file(
+ # Path(output_folder_path) / 'pixel_probabilities' / (fstem + '.tif'),
+ # pxmap
+ # )
+ # ti.click('export_pixel_probability')
obmask = InMemoryDataAccessor(
pxmap.data > pxmap_threshold
@@ -90,7 +90,7 @@ def infer_object_map_from_zstack(
)
ti.click('export_object_classes')
- rois.run_exports(Path(output_folder_path), patches_channel, exports)
+ rois.run_exports(Path(output_folder_path), patches_channel, fstem, exports)
return {
'timer_results': ti.events,
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 3e16b8ad..95d2a73f 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -98,40 +98,41 @@ class RoiSet(object):
def get_object_map(self, filters: RoiFilter):
pass
- def run_exports(self, where, channel, params: RoiSetExportParams):
+ def run_exports(self, where, channel, prefix, params: RoiSetExportParams):
if not self.count:
return
raw_ch = self.acc_raw.get_one_channel_data(channel)
for k in params.dict().keys():
subdir = where / k
+ pr = prefix
kp = params.dict()[k]
if k == 'meta' or kp is None:
continue
- if k == '3d_patches':
+ if k == 'patches_3d':
files = export_patches_from_zstack(
- subdir, raw_ch, self.zmask_meta, prefix=k, make_3d=True, **kp
+ subdir, raw_ch, self.zmask_meta, prefix=pr, make_3d=True, **kp
)
if k == 'patches_2d_for_annotation':
files = export_multichannel_patches_from_zstack(
- subdir, self.acc_raw, self.zmask_meta, prefix=k, make_3d=False, ch_white=channel,
+ subdir, self.acc_raw, self.zmask_meta, prefix=pr, make_3d=False, ch_white=channel,
bounding_box_channel=1, bounding_box_linewidth=2, **kp,
)
if k == 'patches_2d_for_training':
files = export_multichannel_patches_from_zstack(
- subdir, self.acc_raw, self.zmask_meta, ch_white=channel, prefix=k, make_3d=False, **kp
+ subdir, self.acc_raw, self.zmask_meta, ch_white=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['patch_id'] = self.df.apply(lambda _: uuid4(), axis=1)
if k == 'patch_masks':
export_patch_masks_from_zstack(
- subdir, raw_ch, self.zmask_meta, prefix=k,
+ subdir, raw_ch, self.zmask_meta, prefix=pr,
)
if k == 'annotated_zstacks':
annotated = InMemoryDataAccessor(
draw_boxes_on_3d_image(raw_ch.data, self.zmask_meta, **kp)
)
- write_accessor_data_to_file(subdir / (k + '.tif'), annotated)
+ write_accessor_data_to_file(subdir / (pr + '.tif'), annotated)
--
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