From 6a24b7e2c0a17a1177a77250484dd06f6656048c Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 13:42:43 +0100
Subject: [PATCH] Removed direct pixel map access from workflow function
---
extensions/chaeo/params.py | 25 +++++++++-------
extensions/chaeo/tests/test_zstack.py | 16 +++++++----
extensions/chaeo/workflows.py | 41 ++++++++-------------------
extensions/chaeo/zmask.py | 15 +++++-----
4 files changed, 44 insertions(+), 53 deletions(-)
diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index ee4dabd6..5a226925 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -1,4 +1,4 @@
-from typing import Dict, List, Union
+from typing import List, Union
from pydantic import BaseModel
@@ -17,11 +17,22 @@ class PatchParams(BaseModel):
class AnnotatedZStackParams(BaseModel):
draw_label: bool = False
-class RoiSetExportMetaParams(BaseModel):
+class RoiFilterRange(BaseModel):
+ min: float
+ max: float
+
+class RoiFilter(BaseModel):
+ area: Union[RoiFilterRange, None] = None
+ solidity: Union[RoiFilterRange, None] = None
+
+
+class RoiSetMetaParams(BaseModel):
+ mask_type: str = 'boxes'
+ filters: RoiFilter = None
expand_box_by: List[int] = [128, 0]
+
class RoiSetExportParams(BaseModel):
- meta: RoiSetExportMetaParams = RoiSetExportMetaParams()
pixel_probabilities: bool = False
patches_3d: Union[PatchParams, None] = None
patches_2d_for_annotation: Union[PatchParams, None] = None
@@ -30,11 +41,3 @@ class RoiSetExportParams(BaseModel):
annotated_zstacks: Union[AnnotatedZStackParams, None] = None
-class RoiFilterRange(BaseModel):
- min: float
- max: float
-
-
-class RoiFilter(BaseModel):
- area: Union[RoiFilterRange, None] = None
- solidity: Union[RoiFilterRange, None] = None
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index be14b104..9e6e3a74 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -5,7 +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.params import RoiSetExportParams
+from extensions.chaeo.params import RoiSetExportParams, RoiSetMetaParams
from extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack
from extensions.chaeo.workflows import infer_object_map_from_zstack
from extensions.chaeo.zmask import build_zmask_from_object_mask
@@ -208,8 +208,14 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
self.pxmodel,
DummyInstanceSegmentationModel(),
]
+
+ roi_params = RoiSetMetaParams(**{
+ 'mask_type': 'boxes',
+ 'filters': {},
+ 'expand_box_by': [128, 2]
+ })
+
export_params = RoiSetExportParams(**{
- 'expand_box_by': [128, 2],
'pixel_probabilities': True,
'patches_3d': {},
'patches_2d_for_annotation': {
@@ -229,10 +235,10 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
multichannel_zstack['path'],
output_path / 'roiset' / 'workflow',
models,
- pxmap_foreground_channel=pp['pxmap_channel'],
- pxmap_threshold=pp['pxmap_threshold'],
+ pixel_class=pp['pxmap_channel'],
+ pixel_probability_threshold=pp['pxmap_threshold'],
segmentation_channel=pp['segmentation_channel'],
patches_channel=pp['patches_channel'],
- exports=export_params,
+ export_params=export_params,
)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 9171aaa0..4b3f380d 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -9,7 +9,7 @@ from skimage.measure import label, regionprops_table
from skimage.morphology import dilation
from sklearn.model_selection import train_test_split
-from extensions.chaeo.params import RoiSetExportParams
+from extensions.chaeo.params import RoiSetExportParams, RoiSetMetaParams
from extensions.chaeo.process import mask_largest_object
from extensions.chaeo.zmask import RoiSet
@@ -23,15 +23,14 @@ def infer_object_map_from_zstack(
input_file_path: str,
output_folder_path: str,
models: List[Model],
- pxmap_foreground_channel: int,
- pxmap_threshold: float,
segmentation_channel: int,
patches_channel: int,
zmask_zindex: int = None, # None for MIP,
zmask_clip: int = None,
- zmask_type: str = 'boxes',
- zmask_filters: Dict = None,
- exports: RoiSetExportParams = RoiSetExportParams(),
+ roi_params: RoiSetMetaParams = RoiSetMetaParams(),
+ export_params: RoiSetExportParams = RoiSetExportParams(),
+ pixel_class=0,
+ pixel_probability_threshold=0.6,
) -> Dict:
assert len(models) == 2
pixel_classifier = models[0]
@@ -55,29 +54,13 @@ def infer_object_map_from_zstack(
mip = InMemoryDataAccessor(
zmask_data,
)
- 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')
-
- obmask = InMemoryDataAccessor(
- pxmap.data > pxmap_threshold
- )
- ti.click('threshold_pixel_mask')
+ # pxmap, _ = pixel_classifier.infer(mip)
+ mip_mask = pixel_classifier.label_pixel_class(mip, pixel_class, pixel_probability_threshold,)
+ ti.click('classify_pixels')
# make zmask
- rois = RoiSet(
- obmask.get_one_channel_data(pxmap_foreground_channel),
- stack,
- mask_type=zmask_type,
- filters=zmask_filters,
- expand_box_by=exports.meta.expand_box_by,
- )
+ # rois = RoiSet(mip_mask, stack, mask_type=zmask_type, filters=zmask_filters, expand_box_by=meta.expand_box_by)
+ rois = RoiSet(mip_mask, stack, params=roi_params)
ti.click('generate_zmasks')
object_class_map = rois.classify_by(patches_channel, object_classifier)
@@ -90,7 +73,8 @@ def infer_object_map_from_zstack(
)
ti.click('export_object_classes')
- rois.run_exports(Path(output_folder_path), patches_channel, fstem, exports)
+ rois.run_exports(Path(output_folder_path), patches_channel, fstem, export_params)
+ ti.click('export_roi_products')
return {
'timer_results': ti.events,
@@ -100,7 +84,6 @@ def infer_object_map_from_zstack(
}
-
def transfer_ecotaxa_labels_to_patch_stacks(
where_masks: str,
where_patches: str,
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 95d2a73f..900ab02e 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -9,7 +9,7 @@ from sklearn.linear_model import LinearRegression
from extensions.chaeo.annotators import draw_boxes_on_3d_image
from extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack, get_patches_from_zmask_meta, get_patch_masks_from_zmask_meta
-from extensions.chaeo.params import AnnotatedZStackParams, PatchParams, RoiFilter, RoiSetExportParams
+from extensions.chaeo.params import AnnotatedZStackParams, PatchParams, RoiFilter, RoiSetMetaParams, RoiSetExportParams
from extensions.chaeo.process import mask_largest_object
from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.models import InstanceSegmentationModel
@@ -21,16 +21,14 @@ class RoiSet(object):
self,
acc_mask: GenericImageDataAccessor,
acc_raw: GenericImageDataAccessor,
- filters=None,
- mask_type='contours',
- expand_box_by=(0, 0),
+ params: RoiSetMetaParams = RoiSetMetaParams(),
):
self.zmask, self.zmask_meta, self.df, self.interm = build_zmask_from_object_mask(
acc_mask,
acc_raw,
- filters=filters,
- mask_type=mask_type,
- expand_box_by=expand_box_by
+ filters=params.filters,
+ mask_type=params.mask_type,
+ expand_box_by=params.expand_box_by
)
self.acc_raw = acc_raw
@@ -106,7 +104,7 @@ class RoiSet(object):
subdir = where / k
pr = prefix
kp = params.dict()[k]
- if k == 'meta' or kp is None:
+ if kp is None:
continue
if k == 'patches_3d':
files = export_patches_from_zstack(
@@ -136,6 +134,7 @@ class RoiSet(object):
+
def build_zmask_from_object_mask(
obmask: GenericImageDataAccessor,
zstack: GenericImageDataAccessor,
--
GitLab