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Added Parameter for Seg Mask Suffix for Mantis #828

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Nov 15, 2022
Merged

Added Parameter for Seg Mask Suffix for Mantis #828

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16 changes: 11 additions & 5 deletions ark/phenotyping/post_cluster_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,9 @@ def plot_hist_thresholds(cell_table, populations, marker, pop_col='cell_meta_clu
plt.tight_layout()


def create_mantis_project(cell_table, fovs, seg_dir, pop_col, mask_dir, image_dir, mantis_dir):
def create_mantis_project(cell_table, fovs, seg_dir, pop_col,
mask_dir, image_dir, mantis_dir,
seg_suffix_name: str = "_whole_cell") -> None:
"""Create a complete Mantis project for viewing cell labels

Args:
Expand All @@ -60,7 +62,10 @@ def create_mantis_project(cell_table, fovs, seg_dir, pop_col, mask_dir, image_di
pop_col (str): the column containing the distinct cell populations
mask_dir (path): path to the directory where the masks will be stored
image_dir (path): path to the directory containing the raw image data
mantis_dir (path): path to the directory where the mantis project will be created """
mantis_dir (path): path to the directory where the mantis project will be created
seg_suffix_name (str, optional):
The suffix of the segmentation file. Defaults to "_whole_cell".
"""

if not os.path.exists(mask_dir):
os.makedirs(mask_dir)
Expand All @@ -73,12 +78,12 @@ def create_mantis_project(cell_table, fovs, seg_dir, pop_col, mask_dir, image_di

# label and save the cell mask for each FOV
for fov in fovs:
whole_cell_file = [fov + '_whole_cell.tiff' for fov in fovs]
whole_cell_file = [fov + seg_suffix_name + '.tiff' for fov in fovs]

# load the segmentation labels in for the FOV
label_map = load_utils.load_imgs_from_dir(
data_dir=seg_dir, files=whole_cell_file, xr_dim_name='compartments',
xr_channel_names=['whole_cell'], trim_suffix='_whole_cell'
xr_channel_names=[seg_suffix_name], trim_suffix=seg_suffix_name
).loc[fov, ...]

# use label_cells_by_cluster to create cell masks
Expand All @@ -103,4 +108,5 @@ def create_mantis_project(cell_table, fovs, seg_dir, pop_col, mask_dir, image_di
plot_utils.create_mantis_dir(fovs=fovs, mantis_project_path=mantis_dir,
img_data_path=image_dir, mask_output_dir=mask_dir,
mask_suffix='_cell_mask', mapping=mantis_df,
seg_dir=seg_dir, img_sub_folder='')
seg_dir=seg_dir, img_sub_folder='',
seg_suffix_name=seg_suffix_name)
7 changes: 4 additions & 3 deletions ark/phenotyping/post_cluster_utils_test.py
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Expand Up @@ -59,7 +59,7 @@ def test_create_mantis_project(tmp_path):
# create random segmentation masks
for fov in fovs:
data = np.random.randint(0, 5, 100).reshape(10, 10)
io.imsave(os.path.join(seg_dir, fov + '_whole_cell.tiff'), data, check_contrast=False)
io.imsave(os.path.join(seg_dir, fov + '_whole_cell_test.tiff'), data, check_contrast=False)

# create cell table with two clusters
cell_label = np.tile(np.arange(1, 5), len(fovs))
Expand All @@ -72,7 +72,8 @@ def test_create_mantis_project(tmp_path):
post_cluster_utils.create_mantis_project(cell_table=cell_table, fovs=fovs,
seg_dir=seg_dir, pop_col='cell_meta_cluster',
mask_dir=mask_dir, image_dir=image_dir,
mantis_dir=mantis_dir)
mantis_dir=mantis_dir,
seg_suffix_name="_whole_cell_test")

# make sure that the mask found in each mantis directory is correct
for fov in fovs:
Expand All @@ -81,5 +82,5 @@ def test_create_mantis_project(tmp_path):
assert set(np.unique(mask)) == set([0, 1, 2])

# mask should be non-zero in the same places as original
seg = io.imread(os.path.join(seg_dir, fov + '_whole_cell.tiff'))
seg = io.imread(os.path.join(seg_dir, fov + '_whole_cell_test.tiff'))
assert np.array_equal(mask > 0, seg > 0)
10 changes: 7 additions & 3 deletions ark/utils/plot_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -394,7 +394,9 @@ def create_mantis_dir(fovs: List[str], mantis_project_path: Union[str, pathlib.P
mask_output_dir: Union[str, pathlib.Path],
mapping: Union[str, pathlib.Path, pd.DataFrame],
seg_dir: Union[str, pathlib.Path],
mask_suffix: str = "_mask", img_sub_folder: str = ""):
mask_suffix: str = "_mask",
seg_suffix_name: str = "_whole_cell",
img_sub_folder: str = ""):
"""Creates a mantis project directory so that it can be opened by the mantis viewer.
Copies fovs, segmentation files, masks, and mapping csv's into a new directory structure.
Here is how the contents of the mantis project folder will look like.
Expand Down Expand Up @@ -435,6 +437,8 @@ def create_mantis_dir(fovs: List[str], mantis_project_path: Union[str, pathlib.P
The location of the segmentation directory for the fovs.
mask_suffix (str, optional):
The suffix used to find the mask tiffs. Defaults to "_mask".
seg_suffix_name (str, optional):
The suffix of the segmentation file. Defaults to "_whole_cell".
img_sub_folder (str, optional):
The subfolder where the channels exist within the `img_data_path`.
Defaults to "normalized".
Expand Down Expand Up @@ -490,12 +494,12 @@ def create_mantis_dir(fovs: List[str], mantis_project_path: Union[str, pathlib.P
shutil.copy(os.path.join(img_source_dir, chan), os.path.join(output_dir, chan))

# copy mask into new folder
mask_name = mn + mask_suffix + '.tiff'
mask_name: str = mn + mask_suffix + '.tiff'
shutil.copy(os.path.join(mask_output_dir, mask_name),
os.path.join(output_dir, 'population{}.tiff'.format(mask_suffix)))

# copy the segmentation files into the output directory
seg_name = fov + '_whole_cell.tiff'
seg_name: str = fov + seg_suffix_name + '.tiff'
shutil.copy(os.path.join(seg_dir, seg_name),
os.path.join(output_dir, 'cell_segmentation.tiff'))

Expand Down
7 changes: 4 additions & 3 deletions ark/utils/plot_utils_test.py
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Expand Up @@ -2,14 +2,14 @@
import tempfile
from pathlib import Path

import matplotlib.colors as colors
import natsort
import numpy as np
import pandas as pd
import pytest
import skimage.io as io
import xarray as xr
from skimage.draw import disk
import matplotlib.colors as colors

from ark.utils import plot_utils, test_utils

Expand Down Expand Up @@ -299,7 +299,7 @@ def test_create_mantis_dir():

for idx, fov in enumerate(fovs):
# Save the segmentation label compartments for each fov
io.imsave(os.path.join(temp_dir, segmentation_dir, '%s_whole_cell.tiff' % fov),
io.imsave(os.path.join(temp_dir, segmentation_dir, '%s_whole_cell_test.tiff' % fov),
example_labels.loc[idx, ...].values, check_contrast=False)

# Save the sample masks
Expand Down Expand Up @@ -337,6 +337,7 @@ def test_create_mantis_dir():
mask_suffix=mask_suffix,
mapping=mapping,
seg_dir=image_segmentation_full_path,
seg_suffix_name="_whole_cell_test",
img_sub_folder=img_sub_folder
)

Expand All @@ -362,7 +363,7 @@ def test_create_mantis_dir():
# 2.a. Assert that the segmentation label compartments exist in the new directory
assert os.path.exists(cell_seg_path)
original_cell_seg_path = os.path.join(temp_dir, segmentation_dir,
'%s_whole_cell.tiff' % fov)
'%s_whole_cell_test.tiff' % fov)
cell_seg_img = io.imread(cell_seg_path)
original_cell_seg_img = io.imread(original_cell_seg_path)
# 2.b. Assert that the `cell_segmentation` file is equal to `fov#_whole_cell`
Expand Down