From a3043334826dc7589d6d699abb7951a46e4f1353 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 20 Dec 2023 10:01:39 +0100
Subject: [PATCH] Renamed ZMask to RoiSet, prototyped object classification
methods that add classification result as a dataframe column
---
extensions/chaeo/params.py | 25 ++++++++++++++++++++++---
extensions/chaeo/workflows.py | 4 ++--
extensions/chaeo/zmask.py | 29 +++++++++++++++++++++--------
3 files changed, 45 insertions(+), 13 deletions(-)
diff --git a/extensions/chaeo/params.py b/extensions/chaeo/params.py
index 1d03cef5..e516f49b 100644
--- a/extensions/chaeo/params.py
+++ b/extensions/chaeo/params.py
@@ -2,19 +2,22 @@ from typing import Dict, List, Union
from pydantic import BaseModel
+
class PatchParams(BaseModel):
draw_bounding_box: bool = False
draw_contour: bool = False
draw_mask: bool = False
rescale_clip: float = 0.001
focus_metric: str = 'max_sobel'
- rgb_overlay_channels: List[Union[int, None]] = (None, None, None),
- rgb_overlay_weights: List[float] = (1.0, 1.0, 1.0)
+ rgb_overlay_channels: List[Union[int, None]] = [None, None, None]
+ rgb_overlay_weights: List[float] = [1.0, 1.0, 1.0]
+
class AnnotatedZStackParams(BaseModel):
draw_label: bool = False
-class ZMaskExportParams(BaseModel):
+
+class RoiSetExportParams(BaseModel):
pixel_probabilities: bool = False
patches_3d: Union[PatchParams, None] = None
patches_2d_for_annotation: Union[PatchParams, None] = None
@@ -22,3 +25,19 @@ class ZMaskExportParams(BaseModel):
patch_masks: bool = False
annotated_z_stack: Union[AnnotatedZStackParams, None] = None
+
+class RoiClassifierValue(BaseModel):
+ name: str
+ value: int
+
+
+class RoiFilterRange(BaseModel):
+ min: float
+ max: float
+
+
+class RoiFilter(BaseModel):
+ area: Union[RoiFilterRange, None] = None
+ solidity: Union[RoiFilterRange, None] = None
+ classifiers: List[RoiClassifierValue] = []
+
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 7dfe5b84..6e9732f6 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -15,7 +15,7 @@ from extensions.chaeo.models import PatchStackObjectClassifier
from extensions.chaeo.params import ZMaskExportParams
from extensions.chaeo.process import mask_largest_object
from extensions.chaeo.products import export_patches_from_zstack, export_patch_masks_from_zstack, export_multichannel_patches_from_zstack, get_patches_from_zmask_meta, get_patch_masks_from_zmask_meta
-from extensions.chaeo.zmask import project_stack_from_focal_points, ZMaskObjectTable
+from extensions.chaeo.zmask import project_stack_from_focal_points, RoiSet
from extensions.ilastik.models import IlastikPixelClassifierModel
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
@@ -281,7 +281,7 @@ def infer_object_map_from_zstack(
ti.click('threshold_pixel_mask')
# make zmask
- obj_table = ZMaskObjectTable(
+ obj_table = RoiSet(
obmask.get_one_channel_data(pxmap_foreground_channel),
stack.get_one_channel_data(segmentation_channel),
mask_type=zmask_type,
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 04bfeb41..67a78334 100644
--- a/extensions/chaeo/zmask.py
+++ b/extensions/chaeo/zmask.py
@@ -9,12 +9,12 @@ 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
-from extensions.chaeo.params import ZMaskExportParams
+from extensions.chaeo.params import RoiFilter, RoiSetExportParams
from model_server.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
-class ZMaskObjectTable(object):
+class RoiSet(object):
def __init__(
self,
@@ -41,7 +41,7 @@ class ZMaskObjectTable(object):
def get_argmax(self):
return self.interm.argmax
- def export_3d_patches(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_3d_patches(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_patches_from_zstack(
@@ -54,7 +54,7 @@ class ZMaskObjectTable(object):
make_3d=True,
)
- def export_2d_patches_for_annotation(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_2d_patches_for_annotation(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
@@ -78,7 +78,7 @@ class ZMaskObjectTable(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)
- def export_2d_patches_for_training(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_2d_patches_for_training(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
@@ -102,7 +102,7 @@ class ZMaskObjectTable(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)
- def export_2d_patches_for_annotation(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_2d_patches_for_annotation(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
@@ -115,7 +115,7 @@ class ZMaskObjectTable(object):
focus_metric=params.focus_metric,
)
- def export_patch_masks(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_patch_masks(self, where, prefix, channel, params: RoiSetExportParams):
if not self.count:
return
files = export_patch_masks_from_zstack(
@@ -125,7 +125,7 @@ class ZMaskObjectTable(object):
prefix=prefix,
)
- def export_annotated_zstack(self, where, prefix, channel, params: ZMaskExportParams):
+ def export_annotated_zstack(self, where, prefix, channel, params: RoiSetExportParams):
annotated = InMemoryDataAccessor(
draw_boxes_on_3d_image(
self.acc_raw.get_one_channel_data(channel).data,
@@ -152,6 +152,19 @@ class ZMaskObjectTable(object):
projected = self.acc_raw.data.max(axis=-1)
return projected
+ def classify_by(self, column_name, object_classification_model, patch_basis=True):
+ # add one column to df where each value is an integer
+ pass
+
+ def get_raw_patches(self, filters: RoiFilter):
+ pass
+
+ def get_patch_masks(self, filters: RoiFilter):
+ pass
+
+ def get_object_map(self, filters: RoiFilter):
+ pass
+
def build_zmask_from_object_mask(
obmask: GenericImageDataAccessor,
zstack: GenericImageDataAccessor,
--
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