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Fix incomplete_fov_check to not require a channel named Au #474

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Fix incomplete_fov_check to not require a channel named Au #474

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7039f98
Ensure incomplete_fov_check works with first 5 channels irrespective …
alex-l-kong Nov 21, 2024
eb7268b
Fix test to ensure the first two tests work for all channels partiall…
alex-l-kong Nov 21, 2024
15dd93c
Clarify comment
alex-l-kong Nov 21, 2024
73d3770
Merge branch 'main' into remove_au_check
alex-l-kong Nov 21, 2024
951b73d
Merge branch 'main' into remove_au_check
alex-l-kong Dec 4, 2024
89f2820
Merge branch 'main' into remove_au_check
alex-l-kong Dec 5, 2024
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10 changes: 6 additions & 4 deletions src/toffy/bin_extraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,12 +99,14 @@ def incomplete_fov_check(
run_file_path = os.path.join(bin_file_dir, run_name + ".json")
run_metadata = read_json_file(run_file_path, encoding="utf-8")

# get fov and channel info
fovs = io_utils.list_folders(extraction_dir, "fov")
# TODO: list_folders does not handle cases such as "fov0" correctly
# need to add a fix in to alpineer to deal with this
fovs = [f for f in os.listdir(extraction_dir) if "fov" in f]

# NOTE: the specifically-named "Au" channel is no longer be assumed to be present
# simply check the first "num_channels" channels found
channels = io_utils.list_files(os.path.join(extraction_dir, fovs[0]), ".tiff")
channels_subset = channels[:num_channels]
if "Au.tiff" not in channels_subset:
channels_subset = channels_subset[:-1] + ["Au.tiff"]
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Noah specifically noted here that Au should always be a default channel when checking for incomplete fovs. So if some panels don't have gold, then we need this if statement to change instead of removing it completely.
if "Au.tiff" in channels and not in channels_subset:

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@alex-l-kong alex-l-kong Dec 11, 2024 •
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@camisowers in line with adding an explicit argument to set intensity_channels to the callback creation function, what about adding another explicit argument defining a custom name for the gold channel? By default, it will be set to "Au", and even if the user leaves it as None, it'll still assume an "Au.tiff" is found.

In cases where some channels fail to load, instead of erroring out completely, check if the error is specifically caused by a failure to load in gold, and if so, throw a warning that the specific gold channel could not be located and to ask the user to double-check that this is indeed correct.


incomplete_fovs = {}
for fov in fovs:
Expand Down
14 changes: 13 additions & 1 deletion templates/3a_monitor_MIBI_run.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,17 @@
"log_path = os.path.join('C:\\\\Users\\\\Customer.ION\\\\Documents\\\\watcher_logs', run_name)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# define the specific channels you want to extract as intensity images, leave list empty if there are none\n",
"# NOTE: these must match names found in panel_path\n",
"intensity_channels = [\"Au\", \"chan_39\"]"
]
},
{
"cell_type": "markdown",
"metadata": {
Expand Down Expand Up @@ -125,6 +136,7 @@
" save_dir=metrics_plot_dir,\n",
" panel=panel,\n",
" warn_overwrite=False,\n",
" intensities=intensity_channels,\n",
")"
]
},
Expand Down Expand Up @@ -154,7 +166,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.11.9"
},
"vscode": {
"interpreter": {
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28 changes: 25 additions & 3 deletions templates/3b_extract_images_from_bin.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,18 @@
"The function below will skip any previously extracted FOVs and print \"Extraction completed!\" when done. If you receive a warning message stating \"no viable bin files were found\", then all of the necessary FOVs have already been extracted."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "27887a2a-3dc7-4c7a-ac44-e404c29ff112",
"metadata": {},
"outputs": [],
"source": [
"# define the specific channels you want to extract as intensity images, leave list empty if there are none\n",
"# NOTE: these must match names found in panel_path\n",
"intensity_channels = [\"Au\", \"chan_39\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -106,11 +118,21 @@
"outputs": [],
"source": [
"# base deficient extraction\n",
"extract_missing_fovs(base_dir, extraction_dir, panel)\n",
"extract_missing_fovs(\n",
" base_dir,\n",
" extraction_dir,\n",
" panel,\n",
" extract_intensities=intensity_channels,\n",
")\n",
"\n",
"# mass proficient extraction (for long-term storage)\n",
"if extract_prof:\n",
" extract_missing_fovs(base_dir, extraction_prof_dir, modify_panel_ranges(panel, start_offset=0.3, stop_offset=0.3))"
" extract_missing_fovs(\n",
" base_dir,\n",
" extraction_prof_dir,\n",
" modify_panel_ranges(panel, start_offset=0.3, stop_offset=0.3),\n",
" extract_intensities=intensity_channels,\n",
" )"
]
},
{
Expand Down Expand Up @@ -149,7 +171,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.16"
"version": "3.11.9"
}
},
"nbformat": 4,
Expand Down
14 changes: 12 additions & 2 deletions tests/bin_extraction_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,10 +153,15 @@ def test_incomplete_fov_check():

# change fov-2 to have zero values in the bottom of image
fov2_data = load_utils.load_imgs_from_tree(extraction_dir, fovs=["fov-2-scan-1"])
fov2_data[:, 10:, :, 0] = 0
fov2_data_partial = fov2_data.copy()
fov2_data_partial[:, 10:, :, :] = 0
image_utils.save_image(
os.path.join(extraction_dir, "fov-2-scan-1", "Au.tiff"),
fov2_data.loc["fov-2-scan-1", :, :, "Au"],
fov2_data_partial.loc["fov-2-scan-1", :, :, "Au"],
)
image_utils.save_image(
os.path.join(extraction_dir, "fov-2-scan-1", "chan2.tiff"),
fov2_data_partial.loc["fov-2-scan-1", :, :, "chan2"],
)

# test warning for partial fovs (checking 1 channel img)
Expand All @@ -173,6 +178,11 @@ def test_incomplete_fov_check():
)

# test that increasing the number of channels to check causes no warning
# NOTE: this case specifically tests if only a subset of channels are partially imaged
image_utils.save_image(
os.path.join(extraction_dir, "fov-2-scan-1", "chan2.tiff"),
fov2_data.loc["fov-2-scan-1", :, :, "chan2"],
)
with warnings.catch_warnings():
warnings.simplefilter("error")
bin_extraction.incomplete_fov_check(
Expand Down
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