From 9965d5ea2b9486ae705ea8da60ebfd9b272af3be Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sat, 3 Feb 2024 10:22:21 +0100
Subject: [PATCH] Pass RoiSet object to products, much easier
---
model_server/extensions/chaeo/products.py | 40 ++++++++++++++++
.../extensions/chaeo/tests/test_zstack.py | 2 +-
model_server/extensions/chaeo/zmask.py | 46 +++----------------
3 files changed, 47 insertions(+), 41 deletions(-)
diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index ee773a20..d68b4c36 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -57,6 +57,46 @@ def write_patch_to_file(where, fname, yxcz):
raise Exception(f'Unsupported file extension: {ext}')
+def get_patch_masks(roiset, pad_to: int = 256) -> MonoPatchStack:
+
+ patches = []
+ for mi in roiset.zmask_meta:
+ sl = mi['slice']
+
+ rbb = mi['relative_bounding_box']
+ x0 = rbb['x0']
+ y0 = rbb['y0']
+ x1 = rbb['x1']
+ y1 = rbb['y1']
+
+ sp_sl = np.s_[y0: y1, x0: x1, :, :]
+
+ h, w = roiset.acc_raw.data[sl].shape[0:2]
+ patch = np.zeros((h, w, 1, 1), dtype='uint8')
+ patch[sp_sl][:, :, 0, 0] = mi['mask'] * 255
+
+ if pad_to:
+ patch = pad(patch, pad_to)
+
+ patches.append(patch)
+ return MonoPatchStack(patches)
+
+
+def export_patch_masks_from_zstack(roiset, where: Path, pad_to: int = 256, prefix='mask') -> list:
+ patches_acc = roiset.get_patch_masks(pad_to=pad_to)
+
+ exported = []
+ for i in range(0, roiset.count):
+ mi = roiset.zmask_meta[i]
+ obj = mi['info']
+ patch = patches_acc.iat_yxcz(i)
+ ext = 'png'
+ fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
+ write_patch_to_file(where, fname, patch)
+ exported.append(fname)
+ return exported
+
+
def get_patches_from_zmask_meta(
stack: GenericImageDataAccessor,
zmask_meta: list,
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index 66d25594..a925a503 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -199,7 +199,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
filters={'area': {'min': 1e3, 'max': 1e4}},
expand_box_by=(128, 2)
)
- files = roiset.export_patch_masks_from_zstack(output_path / '2d_mask_patches', )
+ files = roiset.export_patch_masks(output_path / '2d_mask_patches', )
self.assertGreaterEqual(len(files), 1)
def test_object_map_workflow(self):
diff --git a/model_server/extensions/chaeo/zmask.py b/model_server/extensions/chaeo/zmask.py
index e30b2c18..1111510c 100644
--- a/model_server/extensions/chaeo/zmask.py
+++ b/model_server/extensions/chaeo/zmask.py
@@ -4,7 +4,6 @@ from math import floor
import numpy as np
import pandas as pd
from pathlib import Path
-from typing import List
from skimage.measure import find_contours, label, regionprops_table
from sklearn.preprocessing import PolynomialFeatures
@@ -19,7 +18,7 @@ from model_server.extensions.chaeo.products import export_patches_from_zstack, e
from extensions.chaeo.params import RoiSetMetaParams, RoiSetExportParams
from model_server.extensions.chaeo.accessors import MonoPatchStack
from model_server.extensions.chaeo.process import mask_largest_object
-from model_server.extensions.chaeo.products import get_patches_from_zmask_meta, write_patch_to_file
+from model_server.extensions.chaeo.products import get_patches_from_zmask_meta, get_patch_masks, export_patch_masks_from_zstack
def get_label_ids(acc_seg_mask):
@@ -62,30 +61,11 @@ class RoiSet(object):
def get_object_mask_by_class(self, class_id):
return self.object_id_labels == class_id
- def get_patch_masks(self, pad_to: int = 256) -> MonoPatchStack:
-
- patches = []
- for mi in self.zmask_meta:
- sl = mi['slice']
-
- rbb = mi['relative_bounding_box']
- x0 = rbb['x0']
- y0 = rbb['y0']
- x1 = rbb['x1']
- y1 = rbb['y1']
-
- sp_sl = np.s_[y0: y1, x0: x1, :, :]
-
- h, w = self.acc_raw.data[sl].shape[0:2]
- patch = np.zeros((h, w, 1, 1), dtype='uint8')
- patch[sp_sl][:, :, 0, 0] = mi['mask'] * 255
-
- if pad_to:
- patch = pad(patch, pad_to)
-
- patches.append(patch)
- return MonoPatchStack(patches)
+ def get_patch_masks(self, **kwargs) -> MonoPatchStack:
+ return get_patch_masks(self, **kwargs)
+ def export_patch_masks(self, where, **kwargs) -> list:
+ return export_patch_masks_from_zstack(self, where, **kwargs)
def get_raw_patches(self, channel):
return get_patches_from_zmask_meta(
@@ -99,20 +79,6 @@ class RoiSet(object):
def get_zmask(self): # TODO: on-the-fly generation of zmask array
return self.zmask
- def export_patch_masks_from_zstack(self, where: Path, pad_to: int = 256, prefix='mask') -> List:
- patches_acc = self.get_patch_masks(pad_to=pad_to)
-
- exported = []
- for i in range(0, self.count):
- mi = self.zmask_meta[i]
- obj = mi['info']
- patch = patches_acc.iat_yxcz(i)
- ext = 'png'
- fname = f'{prefix}-la{obj.label:04d}-zi{obj.zi:04d}.{ext}'
- write_patch_to_file(where, fname, patch)
- exported.append(fname)
- return exported
-
def classify_by(self, channel, object_classification_model: InstanceSegmentationModel):
# do this on a patch basis, i.e. only one object per frame
obmap_patches = object_classification_model.label_instance_class(
@@ -161,7 +127,7 @@ class RoiSet(object):
self.df = pd.merge(self.df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
self.df['patch_id'] = self.df.apply(lambda _: uuid4(), axis=1)
if k == 'patch_masks':
- self.export_patch_masks_from_zstack(subdir, prefix=pr)
+ self.export_patch_masks(subdir, prefix=pr)
if k == 'annotated_zstacks':
annotated = InMemoryDataAccessor(
draw_boxes_on_3d_image(raw_ch.data, self.zmask_meta, **kp)
--
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