From 82e538b208d500002b4b7cd7ea4ec05f78b1ab16 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 9 Oct 2023 17:48:58 +0200
Subject: [PATCH] Export patch masks
---
extensions/chaeo/products.py | 20 +++++++
extensions/chaeo/workflows.py | 108 +++++++++++++++++++---------------
2 files changed, 81 insertions(+), 47 deletions(-)
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index 0595e6a3..87e44073 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -42,6 +42,26 @@ def _write_patch_to_file(where, fname, data):
else:
raise Exception(f'Unsupported file extension: {ext}')
+def export_patch_masks_from_zstack(
+ where: Path,
+ zmask_meta: list,
+ pad_to: int = 256,
+ prefix='mask',
+):
+ exported = []
+ for mi in zmask_meta:
+ obj = mi['info']
+ mask = np.expand_dims(mi['mask'], (2, 3))
+
+ if pad_to:
+ mask = pad(mask, pad_to)
+
+ ext = 'png'
+ fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
+ mask8bit = 255 * mask.astype('uint8')
+ _write_patch_to_file(where, fname, mask8bit)
+ exported.append(fname)
+ return exported
def export_patches_from_zstack(
where: Path,
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 50b9ec52..7f2df928 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -3,7 +3,7 @@ from typing import Dict
from extensions.ilastik.models import IlastikPixelClassifierModel
from extensions.chaeo.annotators import draw_boxes_on_3d_image
-from extensions.chaeo.products import export_patches_from_zstack
+from extensions.chaeo.products import export_patches_from_zstack, export_patch_masks_from_zstack
from extensions.chaeo.zmask import build_zmask_from_object_mask, project_stack_from_focal_points
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.workflows import Timer
@@ -20,6 +20,11 @@ def export_patches_from_multichannel_zstack(
mask_type: str = 'boxes',
zmask_filters: Dict = None,
zmask_expand_box_by: int = None,
+ export_pixel_probabilities=True,
+ export_2d_patches=True,
+ export_3d_patches=True,
+ export_annotated_zstack=True,
+ export_patch_masks=True,
) -> Dict:
ti = Timer()
@@ -38,11 +43,12 @@ def export_patches_from_multichannel_zstack(
pxmap, _ = px_model.infer(mip)
ti.click('infer_pixel_probability')
- write_accessor_data_to_file(
- Path(where_output) / 'pixel_probabilities' / (fstem + '.tif'),
- pxmap
- )
- ti.click('export_pixel_probability')
+ if export_pixel_probabilities:
+ write_accessor_data_to_file(
+ Path(where_output) / 'pixel_probabilities' / (fstem + '.tif'),
+ pxmap
+ )
+ ti.click('export_pixel_probability')
obmask = InMemoryDataAccessor(
pxmap.data > pxmap_threshold
@@ -60,51 +66,59 @@ def export_patches_from_multichannel_zstack(
zmask_acc = InMemoryDataAccessor(zmask)
ti.click('generate_zmasks')
- files = export_patches_from_zstack(
- Path(where_output) / '3d_patches',
- stack.get_one_channel_data(patches_channel),
- zmask_meta,
- prefix=fstem,
- draw_bounding_box=False,
- rescale_clip=0.0,
- make_3d=True,
- )
- ti.click('export_patches')
+ if export_3d_patches:
+ files = export_patches_from_zstack(
+ Path(where_output) / '3d_patches',
+ stack.get_one_channel_data(patches_channel),
+ zmask_meta,
+ prefix=fstem,
+ draw_bounding_box=False,
+ rescale_clip=0.0,
+ make_3d=True,
+ )
+ ti.click('export_3d_patches')
- files = export_patches_from_zstack(
- Path(where_output) / '2d_patches',
- stack.get_one_channel_data(patches_channel),
- zmask_meta,
- prefix=fstem,
- draw_bounding_box=False,
- rescale_clip=0.0,
- make_3d=False,
- focus_metric='max_sobel',
- )
- ti.click('export_patches')
+ if export_2d_patches:
+ files = export_patches_from_zstack(
+ Path(where_output) / '2d_patches',
+ stack.get_one_channel_data(patches_channel),
+ zmask_meta,
+ prefix=fstem,
+ draw_bounding_box=False,
+ rescale_clip=0.0,
+ make_3d=False,
+ focus_metric='max_sobel',
+ )
+ ti.click('export_2d_patches')
- # export annotated zstack
- annotated = InMemoryDataAccessor(
- draw_boxes_on_3d_image(
- stack.get_one_channel_data(patches_channel).data,
- zmask_meta
+ if export_patch_masks:
+ files = export_patch_masks_from_zstack(
+ Path(where_output) / 'patch_masks',
+ zmask_meta,
)
- )
- write_accessor_data_to_file(
- Path(where_output) / 'annotated_zstacks' / (fstem + '.tif'),
- annotated
- )
- ti.click('export_annotated_zstack')
- # # generate multichannel projection from label centroids
- # dff = df[df['keeper']]
- # interm['projected'] = project_stack_from_focal_points(
- # dff['centroid-0'].to_numpy(),
- # dff['centroid-1'].to_numpy(),
- # dff['zi'].to_numpy(),
- # stack,
- # degree=4,
- # )
+ if export_annotated_zstack:
+ annotated = InMemoryDataAccessor(
+ draw_boxes_on_3d_image(
+ stack.get_one_channel_data(patches_channel).data,
+ zmask_meta
+ )
+ )
+ write_accessor_data_to_file(
+ Path(where_output) / 'annotated_zstacks' / (fstem + '.tif'),
+ annotated
+ )
+ ti.click('export_annotated_zstack')
+
+ # generate multichannel projection from label centroids
+ dff = df[df['keeper']]
+ interm['projected'] = project_stack_from_focal_points(
+ dff['centroid-0'].to_numpy(),
+ dff['centroid-1'].to_numpy(),
+ dff['zi'].to_numpy(),
+ stack,
+ degree=4,
+ )
return {
'pixel_model_id': px_model.model_id,
--
GitLab