From efe1e45ce6311f17855031c82cde20de7427a6f2 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 3 Feb 2024 22:47:03 +0100
Subject: [PATCH] Product methods call RoiSet directly; this is causing
problems with multichannel ones where raw data is essentially re-issues to
RGB channels
---
model_server/extensions/chaeo/products.py | 85 ++++++++++---------
.../extensions/chaeo/tests/test_zstack.py | 34 +++++---
model_server/extensions/chaeo/zmask.py | 1 +
3 files changed, 68 insertions(+), 52 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index 3664ce8e..d001114f 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -85,8 +85,9 @@ def export_patch_masks(roiset, where: Path, pad_to: int = 256, prefix='mask') ->
def get_patches_from_zmask_meta(
- stack: GenericImageDataAccessor,
- zmask_meta: list,
+ # stack: GenericImageDataAccessor,
+ # zmask_meta: list,
+ roiset,
rescale_clip: float = 0.0,
pad_to: int = 256,
make_3d: bool = False,
@@ -95,22 +96,23 @@ def get_patches_from_zmask_meta(
) -> MonoPatchStack:
patches = []
- for mi in zmask_meta:
-
- sl = mi['slice']
- rbb = mi['relative_bounding_box'] # TODO: call rel_ fields in DF
- idx = mi['df_index']
-
- x0 = rbb['x0']
- y0 = rbb['y0']
- x1 = rbb['x1']
- y1 = rbb['y1']
-
- sp_sl = np.s_[y0: y1, x0: x1, :, :]
-
- patch3d = stack.data[sl]
+ # for mi in zmask_meta:
+ for i, roi in enumerate(roiset.get_df().itertuples()):
+
+ # sl = roi['slice']
+ # rbb = mi['relative_bounding_box'] # TODO: call rel_ fields in DF
+ # idx = mi['df_index']
+ #
+ # x0 = rbb['x0']
+ # y0 = rbb['y0']
+ # x1 = rbb['x1']
+ # y1 = rbb['y1']
+ #
+ # sp_sl = np.s_[y0: y1, x0: x1, :, :]
+
+ patch3d = roiset.acc_raw.data[roi.slice]
ph, pw, pc, pz = patch3d.shape
- subpatch = patch3d[sp_sl]
+ subpatch = patch3d[roi.relative_slice]
# make a 3d patch
if make_3d:
@@ -133,7 +135,7 @@ def get_patches_from_zmask_meta(
patch = patch3d[:, :, :, [zim]]
assert len(patch.shape) == 4
- assert patch.shape[2] == stack.chroma
+ assert patch.shape[2] == roiset.acc_raw.chroma
if rescale_clip is not None:
patch = rescale(patch, rescale_clip)
@@ -146,21 +148,21 @@ def get_patches_from_zmask_meta(
for zi in range(0, patch.shape[3]):
patch[:, :, bci, zi] = draw_box_on_patch(
patch[:, :, bci, zi],
- ((x0, y0), (x1, y1)),
+ ((roi.rel_x0, roi.rel_y0), (roi.rel_x1, roi.rel_y1)),
linewidth=kwargs.get('bounding_box_linewidth', 1)
)
if kwargs.get('draw_mask'):
mci = kwargs.get('mask_channel', 0)
mask = np.zeros(patch.shape[0:2], dtype=bool)
- mask[sp_sl[0:2]] = mi['mask']
+ mask[roi.relative_slice[0:2]] = roi.mask
for zi in range(0, patch.shape[3]):
patch[:, :, mci, zi] = np.invert(mask) * patch[:, :, mci, zi]
if kwargs.get('draw_contour'):
mci = kwargs.get('contour_channel', 0)
mask = np.zeros(patch.shape[0:2], dtype=bool)
- mask[sp_sl[0:2]] = mi['mask']
+ mask[roi.relative_slice[0:2]] = roi.mask
for zi in range(0, patch.shape[3]):
patch[:, :, mci, zi] = draw_contours_on_patch(
@@ -180,8 +182,9 @@ def get_patches_from_zmask_meta(
def export_patches_from_zstack(
where: Path,
- stack: GenericImageDataAccessor,
- zmask_meta: list,
+ # stack: GenericImageDataAccessor,
+ # zmask_meta: list,
+ roiset,
rescale_clip: float = 0.0,
pad_to: int = 256,
make_3d: bool = False,
@@ -190,24 +193,25 @@ def export_patches_from_zstack(
**kwargs
):
patches_acc = get_patches_from_zmask_meta(
- stack,
- zmask_meta,
- rescale_clip=rescale_clip,
+ roiset,
+ # stack,
+ # zmask_meta,
+ # rescale_clip=rescale_clip,
pad_to=pad_to,
make_3d=make_3d,
focus_metric=focus_metric,
**kwargs
)
- assert len(zmask_meta) == patches_acc.count
exported = []
- for i in range(0, len(zmask_meta)):
- mi = zmask_meta[i]
+ for i, roi in enumerate(roiset.get_df().itertuples()):
+ # for i in range(0, len(zmask_meta)):
+ # mi = zmask_meta[i]
patch = patches_acc.iat_yxcz(i)
- obj = mi['info']
- idx = mi['df_index']
+ # obj = mi['info']
+ # idx = mi['df_index']
ext = 'tif' if make_3d else 'png'
- fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
+ fname = f'{prefix}-la{roi.label:04d}-zi{roi.zi:04d}.{ext}'
if patch.dtype is np.dtype('uint16'):
write_patch_to_file(where, fname, resample_to_8bit(patch))
@@ -215,7 +219,7 @@ def export_patches_from_zstack(
write_patch_to_file(where, fname, patch)
exported.append({
- 'df_index': idx,
+ 'df_index': roi.Index,
'patch_filename': fname,
})
return exported
@@ -303,8 +307,7 @@ def export_3d_patches_with_focus_metrics(
def export_multichannel_patches_from_zstack(
where: Path,
- stack: GenericImageDataAccessor,
- zmask_meta: list,
+ roiset,
rgb_overlay_channels: list = None,
rgb_overlay_weights: list = [1.0, 1.0, 1.0],
ch_white: int = None,
@@ -327,9 +330,9 @@ def export_multichannel_patches_from_zstack(
np.iinfo(a.dtype).max
).astype(a.dtype)
- idata = stack.data
+ idata = roiset.acc_raw.data
if ch_white:
- assert ch_white < stack.chroma
+ assert ch_white < roiset.acc_raw.chroma
mdata = idata[:, :, [ch_white, ch_white, ch_white], :]
else:
mdata = idata
@@ -341,14 +344,14 @@ def export_multichannel_patches_from_zstack(
if ci is None:
continue
assert isinstance(ci, int)
- assert ci < stack.chroma
+ assert ci < roiset.acc_raw.chroma
mdata[:, :, ii, :] = _safe_add(
mdata[:, :, ii, :],
rgb_overlay_weights[ii],
idata[:, :, ci, :]
)
+ # TODO: this is a bit of a workaround
mstack = InMemoryDataAccessor(mdata)
- return export_patches_from_zstack(
- where, mstack, zmask_meta, **kwargs
- )
\ No newline at end of file
+ rgb_roiset = RoiSet(roiset.acc_obj_ids, mstack, roiset.params)
+ return export_patches_from_zstack(where, rgb_roiset, **kwargs)
\ No newline at end of file
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index 6fca51b8..65ecd7b8 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -119,8 +119,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
files = export_patches_from_zstack(
output_path / '2d_patches',
- self.stack_ch_pa,
- roiset.zmask_meta,
+ roiset,
draw_bounding_box=True,
)
self.assertGreaterEqual(len(files), 1)
@@ -132,8 +131,9 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
files = export_patches_from_zstack(
output_path / '3d_patches',
- self.stack_ch_pa,
- roiset.zmask_meta,
+ # self.stack_ch_pa,
+ roiset,
+ # roiset.zmask_meta,
make_3d=True)
self.assertGreaterEqual(len(files), 1)
@@ -162,15 +162,26 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
InMemoryDataAccessor(img)
)
+ def _setup_multichannel_tests(self, mask_type='boxes', **kwargs):
+ id_map = get_label_ids(self.seg_mask)
+ return RoiSet(
+ id_map,
+ self.stack,
+ params=RoiSetMetaParams(
+ mask_type=mask_type, filters=kwargs.get('filters')
+ )
+ )
+
def test_make_multichannel_2d_patches_from_zmask(self):
- roiset = self.test_zmask_makes_correct_boxes(
+ roiset = self._setup_multichannel_tests(
filters={'area': {'min': 1e3, 'max': 1e4}},
expand_box_by=(128, 2)
)
files = export_multichannel_patches_from_zstack(
output_path / '2d_patches_chlorophyl_bbox_overlay',
- InMemoryDataAccessor(self.stack.data),
- roiset.zmask_meta,
+ # InMemoryDataAccessor(self.stack.data),
+ # roiset.zmask_meta,
+ roiset,
ch_white=4,
draw_bounding_box=True,
bounding_box_channel=1,
@@ -184,8 +195,9 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
files = export_multichannel_patches_from_zstack(
output_path / '2d_patches_chlorophyl_mask_overlay',
- InMemoryDataAccessor(self.stack.data),
- roiset.zmask_meta,
+ # InMemoryDataAccessor(self.stack.data),
+ # roiset.zmask_meta,
+ roiset,
ch_white=4,
ch_rgb_overlay=(3, None, None),
draw_mask=True,
@@ -201,8 +213,8 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
files = export_multichannel_patches_from_zstack(
output_path / '2d_patches_chlorophyl_contour_overlay',
- InMemoryDataAccessor(self.stack.data),
- roiset.zmask_meta,
+ # InMemoryDataAccessor(self.stack.data),
+ roiset,
ch_white=4,
ch_rgb_overlay=(3, None, None),
draw_contour=True,
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index 781b6cbc..117e189a 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -34,6 +34,7 @@ class RoiSet(object):
):
self.acc_obj_ids = acc_obj_ids
self.acc_raw = acc_raw
+ self.params = params
self._df = self.filter_df(
self.make_df(
--
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