From 75dca594d3d4d005be6706ab47cf4611d5b9b704 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 1 Aug 2024 12:14:49 +0200
Subject: [PATCH] Test cover use .data_xy and .data_xyz properties
---
model_server/base/accessors.py | 4 ++--
model_server/base/roiset.py | 23 +++++++++++------------
2 files changed, 13 insertions(+), 14 deletions(-)
diff --git a/model_server/base/accessors.py b/model_server/base/accessors.py
index cd35da8a..5be57a4b 100644
--- a/model_server/base/accessors.py
+++ b/model_server/base/accessors.py
@@ -64,14 +64,14 @@ class GenericImageDataAccessor(ABC):
@property
def data_xy(self) -> np.ndarray:
- if not self.nc == 1 and self.nz == 1:
+ if not self.chroma == 1 and self.nz == 1:
raise InvalidDataShape('Can only return XY array from accessors with a single channel and single z-level')
else:
return self.data[:, :, 0, 0]
@property
def data_xyz(self) -> np.ndarray:
- if not self.nc == 1:
+ if not self.chroma == 1:
raise InvalidDataShape('Can only return XYZ array from accessors with a single channel')
else:
return self.data[:, :, 0, :]
diff --git a/model_server/base/roiset.py b/model_server/base/roiset.py
index 12310bec..e28c6645 100644
--- a/model_server/base/roiset.py
+++ b/model_server/base/roiset.py
@@ -71,7 +71,7 @@ def get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, connec
"""
if allow_3d and connect_3d:
nda_la = label(
- acc_seg_mask.data[:, :, 0, :],
+ acc_seg_mask.data_xyz,
connectivity=3,
).astype('uint16')
return InMemoryDataAccessor(np.expand_dims(nda_la, 2))
@@ -80,7 +80,7 @@ def get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, connec
la_3d = np.zeros((*acc_seg_mask.hw, 1, acc_seg_mask.nz), dtype='uint16')
for zi in range(0, acc_seg_mask.nz):
la_2d = label(
- acc_seg_mask.data[:, :, 0, zi],
+ acc_seg_mask.data_xyz[:, :, zi],
connectivity=2,
).astype('uint16')
la_2d[la_2d > 0] = la_2d[la_2d > 0] + nla
@@ -90,7 +90,7 @@ def get_label_ids(acc_seg_mask: GenericImageDataAccessor, allow_3d=False, connec
else:
return InMemoryDataAccessor(
label(
- acc_seg_mask.data[:, :, 0, :].max(axis=-1),
+ acc_seg_mask.data_xyz.max(axis=-1),
connectivity=1,
).astype('uint16')
)
@@ -152,7 +152,7 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
if acc_obj_ids.nz == 1: # deproject objects' z-coordinates from argmax of raw image
df = pd.DataFrame(regionprops_table(
- acc_obj_ids.data[:, :, 0, 0],
+ acc_obj_ids.data_xy,
intensity_image=acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16'),
properties=('label', 'area', 'intensity_mean', 'bbox')
)).rename(columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'y1', 'bbox-3': 'x1'})
@@ -160,7 +160,7 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
else: # objects' z-coordinates come from arg of max count in object identities map
df = pd.DataFrame(regionprops_table(
- acc_obj_ids.data[:, :, 0, :],
+ acc_obj_ids.data_xyz,
properties=('label', 'area', 'bbox')
)).rename(columns={
'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'z0', 'bbox-3': 'y1', 'bbox-4': 'x1', 'bbox-5': 'z1'
@@ -171,7 +171,7 @@ def make_df_from_object_ids(acc_raw, acc_obj_ids, expand_box_by) -> pd.DataFrame
def _make_binary_mask(r):
acc = InMemoryDataAccessor(acc_obj_ids.data == r.label)
- cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data[:, :, 0, 0]
+ cropped = acc.get_mono(0, mip=True).crop_hw((r.y0, r.x0, (r.y1 - r.y0), (r.x1 - r.x0))).data_xy
return cropped
df['binary_mask'] = df.apply(
@@ -581,7 +581,7 @@ class RoiSet(object):
if white_channel:
assert white_channel < raw.chroma
- stack = raw.data[:, :, [white_channel, white_channel, white_channel], :]
+ stack = raw.data[:, :, [white_channel, white_channel, white_channel], :] # TODO: remove direct data access
else:
stack = np.zeros([*raw.shape[0:2], 3, raw.shape[3]], dtype=raw.dtype)
@@ -593,7 +593,7 @@ class RoiSet(object):
stack[:, :, ii, :] = safe_add(
stack[:, :, ii, :], # either black or grayscale channel
rgb_overlay_weights[ii],
- raw.data[:, :, ci, :]
+ raw.get_mono(ci).data_xyz
)
else:
if white_channel is not None: # interpret as just a single channel
@@ -608,9 +608,9 @@ class RoiSet(object):
annotate_rgb = True
break
if annotate_rgb: # make RGB patches anyway to include annotation color
- stack = raw.data[:, :, [white_channel, white_channel, white_channel], :]
+ stack = raw.data[:, :, [white_channel, white_channel, white_channel], :] # TODO: remove direct data access
else: # make monochrome patches
- stack = raw.data[:, :, [white_channel], :]
+ stack = raw.data[:, :, [white_channel], :] # TODO: remove direct data access
elif kwargs.get('channels'):
stack = raw.get_channels(kwargs['channels']).data
else:
@@ -778,7 +778,6 @@ class RoiSet(object):
pad_to = 1
def _poly_from_mask(roi):
- # mask = generate_file_accessor(roi.mask_path).data[:, :, 0, 0]
mask = roi.binary_mask
# label and fill holes
@@ -847,7 +846,7 @@ class RoiSet(object):
try:
ma_acc = generate_file_accessor(where / 'tight_patch_masks' / fname)
assert ma_acc.chroma == 1 and ma_acc.nz == 1
- mask_data = ma_acc.data[:, :, 0, 0] / np.iinfo(ma_acc.data.dtype).max
+ mask_data = ma_acc.data_xy / np.iinfo(ma_acc.data.dtype).max
return mask_data
except Exception as e:
raise DeserializeRoiSet(e)
--
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