From 03d43bf20e32ee73c369206b3ad87244eb680cc9 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 29 Sep 2023 14:55:15 +0200
Subject: [PATCH] Batch export of patches and annotated 2d images is now
working
---
extensions/chaeo/annotators.py | 17 ++--
extensions/chaeo/products.py | 1 -
extensions/chaeo/workflows.py | 91 +++++++++++++++++++
.../ilastik/examples/batch_run_patches.py | 34 +++++++
4 files changed, 136 insertions(+), 7 deletions(-)
create mode 100644 extensions/chaeo/workflows.py
create mode 100644 extensions/ilastik/examples/batch_run_patches.py
diff --git a/extensions/chaeo/annotators.py b/extensions/chaeo/annotators.py
index b0cc1453..eb763feb 100644
--- a/extensions/chaeo/annotators.py
+++ b/extensions/chaeo/annotators.py
@@ -3,8 +3,8 @@ from PIL import Image, ImageDraw, ImageFont
from model_server.process import rescale
-def draw_boxes_on_2d_image(img, boxes, **kwargs):
- pilimg = Image.fromarray(np.copy(img)) # drawing modifies array in-place
+def draw_boxes_on_2d_image(yx_img, boxes, **kwargs):
+ pilimg = Image.fromarray(np.copy(yx_img)) # drawing modifies array in-place
draw = ImageDraw.Draw(pilimg)
font_size = kwargs.get('font_size', 18)
linewidth = kwargs.get('linewidth', 4)
@@ -29,15 +29,20 @@ def draw_boxes_on_2d_image(img, boxes, **kwargs):
return pilimg
-def draw_boxes_on_3d_image(img, boxes, draw_full_depth=False, **kwargs):
- annotated = np.zeros(img.shape, dtype=img.dtype)
+def draw_boxes_on_3d_image(yxcz_img, boxes, draw_full_depth=False, **kwargs):
+ assert len(yxcz_img.shape) == 4
+ nz = yxcz_img.shape[3]
+ assert yxcz_img.shape[2] == 1
+ assert nz > 1
- for zi in range(0, img.shape[0]):
+ annotated = np.zeros(yxcz_img.shape, dtype=yxcz_img.dtype)
+
+ for zi in range(0, nz):
if draw_full_depth:
zi_boxes = boxes
else:
zi_boxes = [bb for bb in boxes if bb['info'].zi == zi]
- annotated[zi, :, :] = draw_boxes_on_2d_image(img[zi, :, :], zi_boxes, **kwargs)
+ annotated[:, :, 0, zi] = draw_boxes_on_2d_image(yxcz_img[:, :, 0, zi], zi_boxes, **kwargs)
if clip := kwargs.get('rescale_clip'):
assert clip >= 0.0 and clip <= 1.0
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index d2a372b0..dd9334a7 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -1,7 +1,6 @@
from pathlib import Path
import numpy as np
-from PIL import Image, ImageDraw
from skimage.io import imsave
from tifffile import imwrite
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
new file mode 100644
index 00000000..9e836713
--- /dev/null
+++ b/extensions/chaeo/workflows.py
@@ -0,0 +1,91 @@
+from pathlib import Path
+from typing import Dict
+
+from pydantic import BaseModel
+
+
+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.zmask import build_zmask_from_object_mask
+from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
+from model_server.workflows import Timer
+
+def export_patches_from_multichannel_zstack( # TODO: PyDantic model for arguments
+ input_zstack_path: Path,
+ px_model: IlastikPixelClassifierModel,
+ pxmap_threshold: float,
+ pixel_class: int,
+ zmask_channel: int,
+ patches_channel: int,
+ where_output: Path,
+ mask_type: str = 'boxes',
+ zmask_filters: Dict = None,
+ zmask_expand_box_by: int = None,
+) -> Dict:
+
+ ti = Timer()
+ stack = generate_file_accessor(input_zstack_path)
+ fstem = input_zstack_path.stem
+ ti.click('file_input')
+ assert stack.nz > 1, 'Expecting z-stack'
+
+ # MIP and classify pixels
+ mip = InMemoryDataAccessor(
+ stack.get_one_channel_data(channel=0).data.max(axis=-1, keepdims=True)
+ )
+ pxmap, _ = px_model.infer(mip)
+ ti.click('infer_pixel_probability')
+
+ write_accessor_data_to_file(
+ where_output / 'pixel_probabilities' / (fstem + '.tif'),
+ pxmap
+ )
+ ti.click('export_pixel_probability')
+
+ obmask = InMemoryDataAccessor(
+ pxmap.data > pxmap_threshold
+ )
+ ti.click('threshold_pixel_mask')
+
+ # make zmask
+ zmask, zmask_meta = build_zmask_from_object_mask(
+ obmask.get_one_channel_data(pixel_class),
+ stack.get_one_channel_data(zmask_channel),
+ mask_type=mask_type,
+ filters=zmask_filters,
+ expand_box_by=zmask_expand_box_by,
+ )
+ zmask_acc = InMemoryDataAccessor(zmask)
+ ti.click('generate_zmasks')
+
+ # export patches
+ files = export_patches_from_zstack(
+ where_output / '2d_patches',
+ stack.get_one_channel_data(patches_channel),
+ zmask_meta,
+ prefix=fstem,
+ draw_bounding_box=True,
+ )
+ ti.click('export_patches')
+
+ # 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(
+ where_output / 'annotated_zstacks' / (fstem + '.tif'),
+ annotated
+ )
+ ti.click('export_annotated_zstack')
+
+ return {
+ 'pixel_model_id': px_model.model_id,
+ 'input_filepath': str(input_zstack_path),
+ 'number_of_objects': len(zmask_meta),
+ 'success': True,
+ 'timer_results': ti.events,
+ }
\ No newline at end of file
diff --git a/extensions/ilastik/examples/batch_run_patches.py b/extensions/ilastik/examples/batch_run_patches.py
new file mode 100644
index 00000000..c985d818
--- /dev/null
+++ b/extensions/ilastik/examples/batch_run_patches.py
@@ -0,0 +1,34 @@
+from pathlib import Path
+
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+from extensions.ilastik.models import IlastikPixelClassifierModel
+
+if __name__ == '__main__':
+ where_czi = Path(
+ 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+ )
+ where_output = Path(
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/batch_output'
+ )
+ px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+ px_model = IlastikPixelClassifierModel(
+ params={'project_file': px_ilp}
+ )
+ for ff in where_czi.iterdir():
+ print(ff)
+ if not ff.suffix.upper() == '.CZI':
+ continue
+
+ export_patches_from_multichannel_zstack(
+ input_zstack_path=where_czi/ff,
+ px_model=px_model,
+ pxmap_threshold=0.6,
+ pixel_class=0,
+ zmask_channel=0,
+ patches_channel=4,
+ where_output=where_output,
+ mask_type='boxes',
+ zmask_filters={'area': (1e2, 1e5)},
+ zmask_expand_box_by=(64, 3),
+ )
+
--
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