From 01adb4b2372fda07c0c75ff89a8cc0dc5e885b20 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 21 Dec 2023 12:03:09 +0100
Subject: [PATCH] Pass params model straight to product exporters, so less code
dedicated to matching parameters
---
extensions/chaeo/annotators.py | 2 +-
extensions/chaeo/products.py | 14 +++++++-------
extensions/chaeo/workflows.py | 1 -
extensions/chaeo/zmask.py | 29 ++++++++++-------------------
4 files changed, 18 insertions(+), 28 deletions(-)
diff --git a/extensions/chaeo/annotators.py b/extensions/chaeo/annotators.py
index eb4996c3..687b4ca1 100644
--- a/extensions/chaeo/annotators.py
+++ b/extensions/chaeo/annotators.py
@@ -23,7 +23,7 @@ def draw_boxes_on_2d_image(yx_img, boxes, **kwargs):
draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=linewidth)
- if kwargs.get('add_label') is True:
+ if kwargs.get('draw_label') is True:
draw.text((xm, y0), f'{la:04d}', fill='white', anchor='mb')
return pilimg
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index 0f1ac976..155a544b 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -331,8 +331,8 @@ def export_multichannel_patches_from_zstack(
where: Path,
stack: GenericImageDataAccessor,
zmask_meta: list,
- ch_rgb_overlay: tuple = None,
- overlay_gain: tuple = (1.0, 1.0, 1.0),
+ rgb_overlay_channels: list = None,
+ rgb_overlay_weights: list = [1.0, 1.0, 1.0],
ch_white: int = None,
**kwargs
):
@@ -360,17 +360,17 @@ def export_multichannel_patches_from_zstack(
else:
mdata = idata
- if ch_rgb_overlay:
- assert len(ch_rgb_overlay) == 3
- assert len(overlay_gain) == 3
- for ii, ci in enumerate(ch_rgb_overlay):
+ if rgb_overlay_channels:
+ assert len(rgb_overlay_channels) == 3
+ assert len(rgb_overlay_weights) == 3
+ for ii, ci in enumerate(rgb_overlay_channels):
if ci is None:
continue
assert isinstance(ci, int)
assert ci < stack.chroma
mdata[:, :, ii, :] = _safe_add(
mdata[:, :, ii, :],
- overlay_gain[ii],
+ rgb_overlay_weights[ii],
idata[:, :, ci, :]
)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 8dd7554f..811aed5f 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -122,7 +122,6 @@ def infer_object_map_from_zstack(
Path(output_folder_path) / 'patch_masks',
fstem,
patches_channel,
- exports.patch_masks
)
if exports.annotated_z_stack:
diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py
index 76e96bf8..77854e3e 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 RoiFilter, RoiSetExportParams
+from extensions.chaeo.params import AnnotatedZStackParams, PatchParams, RoiFilter, 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
@@ -40,7 +40,7 @@ class RoiSet(object):
def get_argmax(self):
return self.interm.argmax
- def export_3d_patches(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_3d_patches(self, where, prefix, channel, params: PatchParams):
if not self.count:
return
files = export_patches_from_zstack(
@@ -48,12 +48,11 @@ class RoiSet(object):
self.acc_raw.get_one_channel_data(channel),
self.zmask_meta,
prefix=prefix,
- draw_bounding_box=params.draw_bounding_box,
- rescale_clip=params.rescale_clip,
make_3d=True,
+ **params.__dict__,
)
- def export_2d_patches_for_training(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_2d_patches_for_training(self, where, prefix, channel, params: PatchParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
@@ -62,15 +61,14 @@ class RoiSet(object):
self.zmask_meta,
ch_white=channel,
prefix=prefix,
- rescale_clip=params.rescale_clip,
make_3d=False,
- focus_metric=params.focus_metric,
+ **params.__dict__,
)
df_patches = pd.DataFrame(files)
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: RoiSetExportParams):
+ def export_2d_patches_for_annotation(self, where, prefix, channel, params: PatchParams):
if not self.count:
return
files = export_multichannel_patches_from_zstack(
@@ -78,21 +76,14 @@ class RoiSet(object):
self.acc_raw,
self.zmask_meta,
prefix=prefix,
- draw_bounding_box=params.draw_bounding_box,
- rescale_clip=params.rescale_clip,
make_3d=False,
- focus_metric=params.focus_metric,
ch_white=channel,
- ch_rgb_overlay=params.rgb_overlay_channels,
bounding_box_channel=1,
bounding_box_linewidth=2,
- draw_contour=params.draw_contour,
- draw_mask=params.draw_mask,
- overlay_gain=params.rgb_overlay_weights,
- pad_to=params.pad_to,
+ **params.__dict__,
)
- def export_patch_masks(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_patch_masks(self, where, prefix, channel):
if not self.count:
return
files = export_patch_masks_from_zstack(
@@ -102,12 +93,12 @@ class RoiSet(object):
prefix=prefix,
)
- def export_annotated_zstack(self, where, prefix, channel, params: RoiSetExportParams):
+ def export_annotated_zstack(self, where, prefix, channel, params: AnnotatedZStackParams):
annotated = InMemoryDataAccessor(
draw_boxes_on_3d_image(
self.acc_raw.get_one_channel_data(channel).data,
self.zmask_meta,
- add_label=params.draw_label,
+ **params.__dict__,
)
)
write_accessor_data_to_file(
--
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