diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index a0f50de3ca097ef1b02a20dd241593bfc8480e83..fa47a57d82cd4e94c699cd86d0ae9659a30c654b 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -1,47 +1,61 @@
-from PIL import Image, ImageDraw, ImageFont
+from pathlib import Path
-def draw_boxes_on_2d_image(img, boxes, **kwargs):
- pilimg = Image.fromarray(np.copy(img)) # drawing modifies array in-place
- draw = ImageDraw.Draw(pilimg)
- font_size = kwargs.get('font_size', 18)
- linewidth = kwargs.get('linewidth', 4)
+import numpy as np
+from PIL import Image, ImageDraw
- draw.font = ImageFont.truetype(font="arial.ttf", size=font_size)
+from skimage.io import imsave
+from tifffile import imwrite
- for box in boxes:
- y0 = box['info'].y0
- y1 = box['info'].y1
- x0 = box['info'].x0
- x1 = box['info'].x1
- xm = round((x0 + x1) / 2)
+from model_server.accessors import GenericImageDataAccessor
+from model_server.process import pad, rescale, resample_to_8bit
- la = box['info'].label
- zi = box['info'].zi
+def _write_patch_to_file(where, fname, data):
+ ext = fname.split('.')[-1].upper()
+ where.mkdir(parents=True, exist_ok=True)
- draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=linewidth)
+ if ext == 'PNG':
+ assert data.dtype == 'uint8', f'Invalid data type {data.dtype}'
+ assert data.shape[2] == 1, f'Cannot export multichannel images as PNGs; RGB not supported'
+ assert data.shape[3] == 1, f'Cannot export z-stacks as PNGs'
+ imsave(where / fname, data[:, :, 0, 0], check_contrast=False)
+ return True
- if kwargs.get('add_label') is True:
- draw.text((xm, y0), f'Z{zi:04d}-L{la:04d}', fill='white', anchor='mb')
+ elif ext in ['TIF', 'TIFF']:
+ zcyx = np.moveaxis(data, [3, 2, 0, 1], [0, 1, 2, 3])
+ imwrite(where / fname, zcyx, imagej=True)
+ return True
- return pilimg
+ else:
+ raise Exception(f'Unsupported file extension: {ext}')
-def generate_patches(
- desc, stack, boxes, rescale_clip=0.0,
- pad_to=256,
- proj=lambda x: x.max(axis=0),
+
+def export_patches_from_zstack(
+ where: Path,
+ stack: GenericImageDataAccessor,
+ zmask_meta: list,
+ rescale_clip: float = 0.0,
+ pad_to: int = 256,
+ make_3d: bool = False,
prefix='patch',
**kwargs
):
- patch_dir = root / 'output' / 'patches' / desc
- patch_dir.mkdir(parents=True, exist_ok=True)
+ assert stack.chroma == 1, 'Expecting monochromatic image data'
+ assert stack.nz > 1, 'Expecting z-stack'
+
+ exported = []
+ for mi in zmask_meta:
+ obj = mi['info']
+ sl = mi['slice']
+ rbb = mi['relative_bounding_box']
- for box in boxes:
- obj = box['info']
- sl = box['slice']
- rbb = box['relative_bounding_box']
+ if make_3d:
+ patch = stack.data[sl]
+ else:
+ patch = np.max(stack.data[sl], axis=3, keepdims=True)
- patch = proj(stack[sl])
- patch_fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}'
+ assert len(patch.shape) == 4
+ assert patch.shape[2] == stack.chroma
+ # assert patch.shape[3] == 1 # should not get to zstacks by this point
if rescale_clip is not None:
patch = rescale(patch, rescale_clip)
@@ -52,46 +66,17 @@ def generate_patches(
x1 = rbb['x1']
y1 = rbb['y1']
- pilimg = Image.fromarray(patch) # drawing modifies array in-place
- draw = ImageDraw.Draw(pilimg)
- draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=kwargs.get('linewidth', 1))
- patch = np.array(pilimg)
+ for zi in range(0, patch.shape[3]):
+ pilimg = Image.fromarray(patch[:, :, 0, zi]) # drawing modifies array in-place
+ draw = ImageDraw.Draw(pilimg)
+ draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=kwargs.get('linewidth', 1))
+ patch[:, :, 0, zi] = np.array(pilimg)
if pad_to:
patch = pad(patch, pad_to)
- imsave(
- patch_dir / (patch_fname + '.png'),
- resample(patch),
- check_contrast=False,
- )
- print(f'Successfully wrote {len(boxes)} patches to:\n{patch_dir}')
-
-
-def generate_3d_patches( # in extensions.chaeo.products
- desc, stack, boxes, rescale_clip=0.0,
- pad_to=256,
- prefix='patch',
- proj=lambda x: x,
-):
- patch_dir = root / 'output' / '3d_patches' / desc
- patch_dir.mkdir(parents=True, exist_ok=True)
-
- for box in boxes:
- obj = box['info']
- sl = box['slice']
- patch = proj(stack[sl])
- patch_fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}'
-
- if rescale_clip is not None:
- patch = rescale(patch, rescale_clip)
-
- if pad_to:
- patch = pad_3d(patch, pad_to)
-
- imwrite(
- patch_dir / (patch_fname + '.tif'),
- patch,
- imagej=True
- )
- print(f'Successfully wrote {len(boxes)} patches to:\n{patch_dir}')
\ No newline at end of file
+ ext = 'tif' if make_3d else 'png'
+ fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
+ success = _write_patch_to_file(where, fname, resample_to_8bit(patch))
+ exported.append(fname)
+ return success, exported
\ No newline at end of file
diff --git a/extensions/chaeo/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
similarity index 70%
rename from extensions/chaeo/test_zstack.py
rename to extensions/chaeo/tests/test_zstack.py
index ebe1172203187b345d9e4b16b35a5f932fd2d3ab..fcbbb3e1fa6dc4502e9326f39d8ff13bc6a2a1b8 100644
--- a/extensions/chaeo/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -5,6 +5,7 @@ import numpy as np
from conf.testing import output_path
from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params
+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 extensions.ilastik.models import IlastikObjectClassifierModel, IlastikPixelClassifierModel
@@ -51,6 +52,8 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
ar = meta[1]['info'].area
self.assertGreaterEqual(sh[0] * sh[1], ar)
+ return zmask, meta
+
def test_zmask_makes_correct_contours(self):
return self.test_zmask_makes_correct_boxes(mask_type='contours')
@@ -58,4 +61,32 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
return self.test_zmask_makes_correct_boxes(filters={'area': (1e3, 1e4)})
def test_zmask_makes_correct_expanded_boxes(self):
- return self.test_zmask_makes_correct_boxes(expand_box_by=(64, 2))
\ No newline at end of file
+ return self.test_zmask_makes_correct_boxes(expand_box_by=(64, 2))
+
+ def test_make_2d_patches_from_zmask(self):
+ zmask, meta = self.test_zmask_makes_correct_boxes(
+ filters={'area': (1e3, 1e4)},
+ expand_box_by=(64, 2)
+ )
+ success, files = export_patches_from_zstack(
+ output_path / '2d_patches',
+ self.stack.get_one_channel_data(channel=1),
+ meta,
+ draw_bounding_box=True,
+ )
+ self.assertTrue(success)
+ self.assertGreaterEqual(len(files), 1)
+
+ def test_make_3d_patches_from_zmask(self):
+ zmask, meta = self.test_zmask_makes_correct_boxes(
+ filters={'area': (1e3, 1e4)},
+ expand_box_by=(64, 2),
+ )
+ success, files = export_patches_from_zstack(
+ output_path / '3d_patches',
+ self.stack.get_one_channel_data(channel=1),
+ meta,
+ make_3d=True)
+ self.assertTrue(success)
+ self.assertGreaterEqual(len(files), 1)
+
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 03188688db74cff9dc168745ac0dbcb2ca61ea42..19c1db5780027be8e734f9403d326158c436e816 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -5,7 +5,6 @@ from skimage.measure import find_contours, label, regionprops_table
from model_server.accessors import GenericImageDataAccessor
-# build a single boolean 3d mask (objects v. bboxes) and return bounding boxes
def build_zmask_from_object_mask(
obmask: GenericImageDataAccessor,
zstack: GenericImageDataAccessor,
@@ -97,7 +96,7 @@ def build_zmask_from_object_mask(
'x1': ob.x1 - x0,
}
- sl = np.s_[y0: y1, x0: x1, 0, z0: z1 + 1]
+ sl = np.s_[y0: y1, x0: x1, :, z0: z1 + 1]
# compute contours
obmask = (lamap == ob.label)