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Contains scripts and little tools which are used throughout ark-analysis, mibi-bin-tools, and toffy." +category = "main" optional = false python-versions = ">=3.9,<4.0" files = [ @@ -41,9 +44,9 @@ files = [ charset-normalizer = ">=2.1.1,<3.0.0" matplotlib = ">=3,<4" natsort = ">=8,<9" -numpy = "==1.*" +numpy = ">=1.0.0,<2.0.0" pillow = ">=9,<10" -scikit-image = "==0.*" +scikit-image = "<1.0.0" tifffile = "*" xarray = "*" xmltodict = ">=0.13.0,<0.14.0" @@ -52,6 +55,7 @@ xmltodict = ">=0.13.0,<0.14.0" name = "anyio" version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -73,6 +77,7 @@ trio = ["trio (<0.22)"] name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" +category = "main" optional = false python-versions = "*" files = [ @@ -84,6 +89,7 @@ files = [ name = "argon2-cffi" version = "21.3.0" description = "The secure Argon2 password hashing algorithm." +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -103,6 +109,7 @@ tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -140,6 +147,7 @@ tests = ["pytest"] name = "arrow" version = "1.2.3" description = "Better dates & times for Python" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -154,6 +162,7 @@ python-dateutil = ">=2.7.0" name = "asttokens" version = "2.2.1" description = "Annotate AST trees with source code positions" +category = "main" optional = false python-versions = "*" files = [ @@ -171,6 +180,7 @@ test = ["astroid", "pytest"] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -189,6 +199,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.12.1" description = "Internationalization utilities" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -200,6 +211,7 @@ files = [ name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" +category = "main" optional = false python-versions = "*" files = [ @@ -211,6 +223,7 @@ files = [ name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "dev" optional = false python-versions = ">=3.6.0" files = [ @@ -229,6 +242,7 @@ lxml = ["lxml"] name = "black" version = "22.12.0" description = "The uncompromising code formatter." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -264,6 +278,7 @@ uvloop = ["uvloop (>=0.15.2)"] name = "bleach" version = "6.0.0" description = "An easy safelist-based HTML-sanitizing tool." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -280,19 +295,21 @@ css = ["tinycss2 (>=1.1.0,<1.2)"] [[package]] name = "certifi" -version = "2023.5.7" +version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." +category = "dev" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"}, - {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"}, + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, ] [[package]] name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." +category = "main" optional = false python-versions = "*" files = [ @@ -369,6 +386,7 @@ pycparser = "*" name = "charset-normalizer" version = "2.1.1" description = "The Real First Universal Charset Detector. 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= "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"}, - {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"}, + {file = "importlib_resources-6.0.0-py3-none-any.whl", hash = "sha256:d952faee11004c045f785bb5636e8f885bed30dc3c940d5d42798a2a4541c185"}, + {file = "importlib_resources-6.0.0.tar.gz", hash = "sha256:4cf94875a8368bd89531a756df9a9ebe1f150e0f885030b461237bc7f2d905f2"}, ] [package.dependencies] zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [[package]] name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -864,6 +961,7 @@ files = [ name = "ipykernel" version = "6.24.0" description = "IPython Kernel for Jupyter" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -877,7 +975,7 @@ comm = ">=0.1.1" debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" @@ -897,6 +995,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio" name = "ipython" version = "8.14.0" description = "IPython: Productive Interactive Computing" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -936,6 +1035,7 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "ipython-genutils" version = "0.2.0" description = "Vestigial utilities from IPython" +category = "dev" optional = false python-versions = "*" files = [ @@ -947,6 +1047,7 @@ files = [ name = "ipywidgets" version = "8.0.7" description = "Jupyter interactive widgets" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -968,6 +1069,7 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -982,6 +1084,7 @@ arrow = ">=0.15.0" name = "isort" version = "5.12.0" description = "A Python utility / library to sort Python imports." +category = "dev" optional = false python-versions = ">=3.8.0" files = [ @@ -999,6 +1102,7 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] name = "jedi" version = "0.18.2" description = "An autocompletion tool for Python that can be used for text editors." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1018,6 +1122,7 @@ testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1035,6 +1140,7 @@ i18n = ["Babel (>=2.7)"] name = "joblib" version = "1.3.1" description = "Lightweight pipelining with Python functions" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1046,6 +1152,7 @@ files = [ name = "json5" version = "0.9.14" description = "A Python implementation of the JSON5 data format." +category = "dev" optional = false python-versions = "*" files = [ @@ -1060,6 +1167,7 @@ dev = ["hypothesis"] name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1069,24 +1177,27 @@ files = [ [[package]] name = "jsonschema" -version = "4.17.3" +version = "4.18.4" description = "An implementation of JSON Schema validation for Python" +category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"}, - {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"}, + {file = "jsonschema-4.18.4-py3-none-any.whl", hash = "sha256:971be834317c22daaa9132340a51c01b50910724082c2c1a2ac87eeec153a3fe"}, + {file = "jsonschema-4.18.4.tar.gz", hash = "sha256:fb3642735399fa958c0d2aad7057901554596c63349f4f6b283c493cf692a25d"}, ] [package.dependencies] -attrs = ">=17.4.0" +attrs = ">=22.2.0" fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""} -pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" +jsonschema-specifications = ">=2023.03.6" +referencing = ">=0.28.4" rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""} +rpds-py = ">=0.7.1" uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""} @@ -1094,10 +1205,26 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-n format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] +[[package]] +name = "jsonschema-specifications" +version = "2023.7.1" +description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "dev" +optional = false +python-versions = ">=3.8" +files = [ + {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"}, + {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"}, +] + +[package.dependencies] +referencing = ">=0.28.0" + [[package]] name = "jupyter-client" version = "8.3.0" description = "Jupyter protocol implementation and client libraries" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1107,7 +1234,7 @@ files = [ [package.dependencies] importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -1121,6 +1248,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt name = "jupyter-contrib-core" version = "0.4.2" description = "Common utilities for jupyter-contrib projects." +category = "dev" optional = false python-versions = "*" files = [ @@ -1141,6 +1269,7 @@ testing-utils = ["mock", "nose"] name = "jupyter-contrib-nbextensions" version = "0.7.0" description = "A collection of Jupyter nbextensions." +category = "dev" optional = false python-versions = "*" files = [ @@ -1166,6 +1295,7 @@ test = ["mock", "nbformat", "nose", "pip", "requests"] name = "jupyter-core" version = "5.3.1" description = "Jupyter core package. A base package on which Jupyter projects rely." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1186,6 +1316,7 @@ test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] name = "jupyter-events" version = "0.6.3" description = "Jupyter Event System library" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1210,6 +1341,7 @@ test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>= name = "jupyter-highlight-selected-word" version = "0.2.0" description = "Jupyter notebook extension that enables highlighting every instance of the current word in the notebook." +category = "dev" optional = false python-versions = "*" files = [ @@ -1221,6 +1353,7 @@ files = [ name = "jupyter-nbextensions-configurator" version = "0.6.3" description = "jupyter serverextension providing configuration interfaces for nbextensions." +category = "dev" optional = false python-versions = "*" files = [ @@ -1242,6 +1375,7 @@ test = ["jupyter-contrib-core[testing-utils]", "mock", "nose", "requests", "sele name = "jupyter-server" version = "2.7.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1254,7 +1388,7 @@ anyio = ">=3.1.0" argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" -jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" jupyter-events = ">=0.6.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" @@ -1278,6 +1412,7 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc name = "jupyter-server-fileid" version = "0.9.0" description = "" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1297,6 +1432,7 @@ test = ["jupyter-server[test] (>=1.15,<3)", "pytest", "pytest-cov"] name = "jupyter-server-terminals" version = "0.4.4" description = "A Jupyter Server Extension Providing Terminals." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1316,6 +1452,7 @@ test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", name = "jupyter-server-ydoc" version = "0.8.0" description = "A Jupyter Server Extension Providing Y Documents." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1333,27 +1470,29 @@ test = ["coverage", "jupyter-server[test] (>=2.0.0a0)", "pytest (>=7.0)", "pytes [[package]] name = "jupyter-ydoc" -version = "0.2.4" +version = "0.2.5" description = "Document structures for collaborative editing using Ypy" +category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "jupyter_ydoc-0.2.4-py3-none-any.whl", hash = "sha256:d1a51c73ead6f6417bec0450f53c577a66abe8d43e9c2d8a1acaf7a17259f843"}, - {file = "jupyter_ydoc-0.2.4.tar.gz", hash = "sha256:a3f670a69135e90493ffb91d6788efe2632bf42c6cc42a25f25c2e6eddd55a0e"}, + {file = "jupyter_ydoc-0.2.5-py3-none-any.whl", hash = "sha256:5759170f112c70320a84217dd98d287699076ae65a7f88d458d57940a9f2b882"}, + {file = "jupyter_ydoc-0.2.5.tar.gz", hash = "sha256:5a02ca7449f0d875f73e8cb8efdf695dddef15a8e71378b1f4eda6b7c90f5382"}, ] [package.dependencies] importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} -y-py = ">=0.5.3,<0.6.0" +y-py = ">=0.6.0,<0.7.0" [package.extras] dev = ["click", "jupyter-releaser"] -test = ["pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)", "ypy-websocket (>=0.3.1,<0.4.0)"] +test = ["pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)", "ypy-websocket (>=0.8.4,<0.9.0)"] [[package]] name = "jupyterlab" version = "3.6.5" description = "JupyterLab computational environment" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1382,6 +1521,7 @@ test = ["check-manifest", "coverage", "jupyterlab-server[test]", "pre-commit", " name = "jupyterlab-pygments" version = "0.2.2" description = "Pygments theme using JupyterLab CSS variables" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1391,13 +1531,14 @@ files = [ [[package]] name = "jupyterlab-server" -version = "2.23.0" +version = "2.24.0" description = "A set of server components for JupyterLab and JupyterLab like applications." +category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "jupyterlab_server-2.23.0-py3-none-any.whl", hash = "sha256:a5ea2c839336a8ba7c38c8e7b2f24cedf919f0d439f4d2e606d9322013a95788"}, - {file = "jupyterlab_server-2.23.0.tar.gz", hash = "sha256:83c01aa4ad9451cd61b383e634d939ff713850f4640c0056b2cdb2b6211a74c7"}, + {file = "jupyterlab_server-2.24.0-py3-none-any.whl", hash = "sha256:5f077e142bb8dc9b843d960f940c513581bceca3793a0d80f9c67d9522c4e876"}, + {file = "jupyterlab_server-2.24.0.tar.gz", hash = "sha256:4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07"}, ] [package.dependencies] @@ -1413,12 +1554,13 @@ requests = 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["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.12" -content-hash = "2fe07f2c6eb19f355a5dd660202faf5465ebcc36ad7beb2212588b1ec62e1ea1" +content-hash = "df51137177a85a2f22a8d85d3efc048f58ae4df0c74636088aa093e8d1288d25" diff --git a/pyproject.toml b/pyproject.toml index 5a15e8ff..a7d35144 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ metadata = false [tool.poetry.dependencies] python = ">=3.9,<3.12" alpineer = ">=0.1.9" -mibi-bin-tools = "0.2.9" +mibi-bin-tools = "0.2.10" ipywidgets = "^8" numpy = "1.*" natsort = "^8" diff --git a/src/toffy/normalize.py b/src/toffy/normalize.py index 2921d116..1a1c2c23 100644 --- a/src/toffy/normalize.py +++ b/src/toffy/normalize.py @@ -47,7 +47,9 @@ def write_counts_per_mass(base_dir, output_dir, fov, masses, start_offset=0.5, s out_df.to_csv(os.path.join(output_dir, fov + "_channel_counts.csv"), index=False) -def write_mph_per_mass(base_dir, output_dir, fov, masses, start_offset=0.5, stop_offset=0.5): +def write_mph_per_mass( + base_dir, output_dir, fov, masses, start_offset=0.5, stop_offset=0.5, proficient=False +): """Records the median pulse height (MPH) per mass for the specified FOV Args: @@ -57,6 +59,7 @@ def write_mph_per_mass(base_dir, output_dir, fov, masses, start_offset=0.5, stop masses (list): the list of masses to extract MPH from start_offset (float): beginning value for calculating mph values stop_offset (float): ending value for calculating mph values + proficient (bool): whether proficient MPH data is written or not """ # hold computed values mph_vals = [] @@ -72,7 +75,10 @@ def write_mph_per_mass(base_dir, output_dir, fov, masses, start_offset=0.5, stop # create df to hold output fovs = np.repeat(fov, len(masses)) out_df = pd.DataFrame({"mass": masses, "fov": fovs, "pulse_height": mph_vals}) - out_df.to_csv(os.path.join(output_dir, fov + "_pulse_heights.csv"), index=False) + pulse_heights_file = ( + fov + "_pulse_heights_proficient.csv" if proficient else fov + "_pulse_heights.csv" + ) + out_df.to_csv(os.path.join(output_dir, pulse_heights_file), index=False) def create_objective_function(obj_func): @@ -222,7 +228,9 @@ def combine_run_metrics(run_dir, substring, warn_overwrite=True): substring(str): the substring contained within the files to be combined warn_overwrite (bool): whether to warn if existing `_combined.csv` file found""" + # retrieve all pulse height files, but ignore anything mass proficient files = io_utils.list_files(run_dir, substring) + files = [file for file in files if "_proficient" not in file] # validate inputs if len(files) == 0: diff --git a/src/toffy/panel_utils.py b/src/toffy/panel_utils.py index a08728f0..9abb3d3e 100644 --- a/src/toffy/panel_utils.py +++ b/src/toffy/panel_utils.py @@ -105,6 +105,41 @@ ) +def modify_panel_ranges(panel: pd.DataFrame, start_offset: float = 0, stop_offset: float = 0): + """Adjust the offsets of a given panel. + + Only applicable for masses with ranges separated by 0.3 between 'Stop' and 'Start'. + + Args: + panel (pd.DataFrame): panel dataframe with columns Mass, Target, Start, and Stop. + start_offset (float): the value to add to the `'Start'` column. + stop_offset (float): the value to add to the `'Stop'` column. + + Returns: + pd.DataFrame: + Updated panel with `start_offset` added to `'Start`' column, + likewise for `stop_offset` and `'Stop'` column. + """ + panel_new = panel.copy() + + # extract only rows where 'Start' - 'End' = -0.3, round to account for floating point error + panel_rows_modify = panel_new[ + (panel_new["Start"] - panel_new["Stop"]).round(1) == -0.3 + ].index.values + + # add start_offset to 'Start' column + panel_new.loc[panel_rows_modify, "Start"] = ( + panel_new.loc[panel_rows_modify, "Start"].copy() + start_offset + ) + + # add stop_offset to 'Stop' column + panel_new.loc[panel_rows_modify, "Stop"] = ( + panel_new.loc[panel_rows_modify, "Stop"].copy() + stop_offset + ) + + return panel_new + + def merge_duplicate_masses(panel): """Check a panel df for duplicate mass values and return a unique mass panel with the target names combined diff --git a/src/toffy/watcher_callbacks.py b/src/toffy/watcher_callbacks.py index cd3648bf..c82b25be 100644 --- a/src/toffy/watcher_callbacks.py +++ b/src/toffy/watcher_callbacks.py @@ -18,6 +18,7 @@ from toffy.image_stitching import stitch_images from toffy.mph_comp import combine_mph_metrics, compute_mph_metrics, visualize_mph from toffy.normalize import write_mph_per_mass +from toffy.panel_utils import modify_panel_ranges from toffy.qc_comp import combine_qc_metrics, compute_qc_metrics_direct from toffy.qc_metrics_plots import visualize_qc_metrics from toffy.settings import QC_COLUMNS @@ -124,11 +125,14 @@ class FovCallbacks: point_name: str overwrite: bool __panel: pd.DataFrame = field(default=None, init=False) + __panel_prof: pd.DataFrame = field(default=None, init=False) __fov_data: xr.DataArray = field(default=None, init=False) + __fov_data_prof: xr.DataArray = field(default=None, init=False) def _generate_fov_data( self, panel: pd.DataFrame, + extract_prof: bool, intensities=["Au", "chan_39"], replace=True, time_res=0.0005, @@ -138,9 +142,13 @@ def _generate_fov_data( The data and the panel are then cached members of the FovCallbacks object + Both the deficient and proficient extracted data and panel are computed and cached + Args: panel (pd.DataFrame): Panel used for extraction + extract_prof (bool): + If set, extract proficient data intensities (bool | List[str]): Intensities argument for `mibi_bin_tools.bin_files.extract_bin_files` replace (bool): @@ -159,17 +167,37 @@ def _generate_fov_data( replace=replace, time_res=time_res, ) - self.__panel = panel - def extract_tiffs(self, tiff_out_dir: str, panel: pd.DataFrame, **kwargs): + if extract_prof: + # adds an offset of 0.3 to 'Start' and 'Stop' columns, modifying extraction range + # from (-0.3, 0) to (0, 0.3) for proficient extraction + panel_prof = modify_panel_ranges(panel, start_offset=0.3, stop_offset=0.3) + self.__fov_data_prof = extract_bin_files( + data_dir=self.run_folder, + out_dir=None, + include_fovs=[self.point_name], + panel=panel_prof, + intensities=intensities, + replace=replace, + time_res=time_res, + ) + self.__panel_prof = panel_prof + + def extract_tiffs( + self, tiff_out_dir: str, panel: pd.DataFrame, extract_prof: bool = True, **kwargs + ): """Extract tiffs into provided directory, using given panel + Done for both the extracted deficient and proficient data + Args: tiff_out_dir (str): Path where tiffs are written panel (pd.DataFrame): Target mass integration ranges + extract_prof (bool): + If set, extract mass proficient data **kwargs (dict): Additional arguments for `mibi_bin_tools.bin_files.extract_bin_files`. Accepted kwargs are @@ -199,8 +227,8 @@ def extract_tiffs(self, tiff_out_dir: str, panel: pd.DataFrame, **kwargs): unextracted_chans = io_utils.remove_file_extensions(unextracted_chan_tiffs) panel = panel[panel["Target"].isin(unextracted_chans)] - if self.__fov_data is None: - self._generate_fov_data(panel, **kwargs) + if self.__fov_data is None or self.__fov_data_prof is None: + self._generate_fov_data(panel, extract_prof, **kwargs) intensities = kwargs.get("intensities", ["Au", "chan_39"]) if any_true(intensities) and type(intensities) is not list: @@ -214,7 +242,18 @@ def extract_tiffs(self, tiff_out_dir: str, panel: pd.DataFrame, **kwargs): intensities=intensities, ) - def generate_qc(self, qc_out_dir: str, panel: pd.DataFrame = None, **kwargs): + if extract_prof: + _write_out( + img_data=self.__fov_data_prof[0, :, :, :, :].values, + out_dir=tiff_out_dir + "_proficient", + fov_name=self.point_name, + targets=list(self.__fov_data.channel.values), + intensities=intensities, + ) + + def generate_qc( + self, qc_out_dir: str, panel: pd.DataFrame = None, extract_prof: bool = True, **kwargs + ): """Generates qc metrics from given panel, and saves output to provided directory Args: @@ -222,6 +261,8 @@ def generate_qc(self, qc_out_dir: str, panel: pd.DataFrame = None, **kwargs): Path where qc_metrics are written panel (pd.DataFrame): Target mass integration ranges + extract_prof (bool): + If set, extract mass proficient data **kwargs (dict): Additional arguments for `toffy.qc_comp.compute_qc_metrics`. Accepted kwargs are: @@ -234,7 +275,7 @@ def generate_qc(self, qc_out_dir: str, panel: pd.DataFrame = None, **kwargs): if self.__fov_data is None: if panel is None: raise ValueError("Must provide panel if fov data is not already generated...") - self._generate_fov_data(panel, **kwargs) + self._generate_fov_data(panel, extract_prof, **kwargs) qc_metric_paths = [ os.path.join(qc_out_dir, f"{self.point_name}_nonzero_mean_stats.csv"), @@ -267,7 +308,6 @@ def generate_mph(self, mph_out_dir, **kwargs): - mass_start - mass_stop """ - if not os.path.exists(mph_out_dir): os.makedirs(mph_out_dir) @@ -297,7 +337,6 @@ def generate_pulse_heights(self, pulse_out_dir: str, panel: pd.DataFrame = None, - start_offset - stop_offset """ - if not os.path.exists(pulse_out_dir): os.makedirs(pulse_out_dir) @@ -422,7 +461,6 @@ def run_callback(run_folder: str): # unreachable... raise ValueError(f"Could not locate attribute {run_cb} in RunCallbacks object") - intermediate_callback = None intermediate_callback = None if intermediate_callbacks: diff --git a/templates/3a_monitor_MIBI_run.ipynb b/templates/3a_monitor_MIBI_run.ipynb index b04af332..c32dfb87 100644 --- a/templates/3a_monitor_MIBI_run.ipynb +++ b/templates/3a_monitor_MIBI_run.ipynb @@ -30,7 +30,8 @@ "## Required variables\n", "\n", " - `run_name` should contain the exact name of the MIBI run that will be monitored\n", - " - `panel_path` should point to a panel csv specifying the targets on your panel. You can download your panel online from the Ionpath MibiTracker and then copy the file to the `C:\\\\Users\\\\Customer.ION\\\\Documents\\panel_files` directory (see [panel format](https://github.com/angelolab/toffy#panel-format) for more information)" + " - `panel_path` should point to a panel csv specifying the targets on your panel. You can download your panel online from the Ionpath MibiTracker and then copy the file to the `C:\\\\Users\\\\Customer.ION\\\\Documents\\panel_files` directory (see [panel format](https://github.com/angelolab/toffy#panel-format) for more information)\n", + " - `extract_prof` indicates whether you want to include mass proficient extraction on top of the default (mass deficient) extraction" ] }, { @@ -43,7 +44,10 @@ "run_name = 'YYYY-MM-DD_run_name'\n", "\n", "# path to user panel\n", - "panel_path = 'C:\\\\Users\\\\Customer.ION\\\\Documents\\\\panel_files\\\\my_cool_panel.csv'" + "panel_path = 'C:\\\\Users\\\\Customer.ION\\\\Documents\\\\panel_files\\\\my_cool_panel.csv'\n", + "\n", + "# whether to include proficient extraction or not\n", + "extract_prof = True" ] }, { @@ -106,6 +110,7 @@ " run_callbacks = ['image_stitching'],\n", " intermediate_callbacks = ['plot_qc_metrics', 'plot_mph_metrics'],\n", " fov_callbacks = ['extract_tiffs', 'generate_pulse_heights'],\n", + " extract_prof=extract_prof,\n", " tiff_out_dir=extraction_dir,\n", " qc_out_dir=metrics_data_dir,\n", " mph_out_dir=metrics_data_dir,\n", diff --git a/templates/3b_extract_images_from_bin.ipynb b/templates/3b_extract_images_from_bin.ipynb index abeda208..f3cae308 100644 --- a/templates/3b_extract_images_from_bin.ipynb +++ b/templates/3b_extract_images_from_bin.ipynb @@ -23,7 +23,7 @@ "source": [ "import os\n", "\n", - "from toffy.panel_utils import load_panel\n", + "from toffy.panel_utils import modify_panel_ranges, load_panel\n", "from toffy.bin_extraction import extract_missing_fovs" ] }, @@ -35,7 +35,8 @@ "## Required variables\n", "You will need to define the following two arguments for this notebook.\n", " - `run_name` should contain the exact name of the MIBI run to extract from\n", - " - `panel_path` should point to a panel csv specifying the targets on your panel. You can download your panel online from the Ionpath MibiTracker and then copy the file to the `C:\\\\Users\\\\Customer.ION\\\\Documents\\panel_files` directory (see [panel format](https://github.com/angelolab/toffy#panel-format) for more information)" + " - `panel_path` should point to a panel csv specifying the targets on your panel. You can download your panel online from the Ionpath MibiTracker and then copy the file to the `C:\\\\Users\\\\Customer.ION\\\\Documents\\panel_files` directory (see [panel format](https://github.com/angelolab/toffy#panel-format) for more information)\n", + " - `extract_prof` indicates whether you want to include mass proficient extraction on top of the default (mass deficient) extraction" ] }, { @@ -49,7 +50,8 @@ "source": [ "# set up args for current run\n", "run_name = 'YYYY-MM-DD_run_name'\n", - "panel_path = 'C:\\\\Users\\\\Customer.ION\\\\Documents\\\\panel_files\\\\my_cool_panel.csv'" + "panel_path = 'C:\\\\Users\\\\Customer.ION\\\\Documents\\\\panel_files\\\\my_cool_panel.csv'\n", + "extract_prof = True" ] }, { @@ -78,7 +80,13 @@ "# path to directory containing extracted files\n", "extraction_dir = os.path.join('D:\\\\Extracted_Images', run_name) \n", "if not os.path.exists(extraction_dir):\n", - " os.makedirs(extraction_dir)" + " os.makedirs(extraction_dir)\n", + "\n", + "if extract_prof:\n", + " # path to directory containing mass-proficient extracted files (for long-term storage)\n", + " extraction_prof_dir = os.path.join('D:\\\\Extracted_Images', run_name + '_proficient')\n", + " if not os.path.exists(extraction_prof_dir):\n", + " os.makedirs(extraction_prof_dir)" ] }, { @@ -97,7 +105,12 @@ "metadata": {}, "outputs": [], "source": [ - "extract_missing_fovs(base_dir, extraction_dir, panel)" + "# base deficient extraction\n", + "extract_missing_fovs(base_dir, extraction_dir, panel)\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))" ] } ], @@ -117,7 +130,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.16" + "version": "3.9.16" } }, "nbformat": 4, diff --git a/templates/4b_normalize_image_data.ipynb b/templates/4b_normalize_image_data.ipynb index 2bfe9ec0..0f6798fa 100644 --- a/templates/4b_normalize_image_data.ipynb +++ b/templates/4b_normalize_image_data.ipynb @@ -137,6 +137,8 @@ "for fov in fovs:\n", " # generate mph values\n", " mph_file_path = os.path.join(mph_run_dir, fov + '_pulse_heights.csv')\n", + " \n", + " # base MPH normalization\n", " if not os.path.exists(mph_file_path):\n", " normalize.write_mph_per_mass(base_dir=os.path.join(bin_base_dir, run_name), output_dir=mph_run_dir, \n", " fov=fov, masses=panel['Mass'].values, start_offset=0.3, stop_offset=0)" diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py index e64d5e85..cc4b76d6 100644 --- a/tests/fov_watcher_test.py +++ b/tests/fov_watcher_test.py @@ -242,6 +242,7 @@ def test_watcher( add_blank, temp_bin, ): + print("The watcher start lag is: %d" % watcher_start_lag) try: with tempfile.TemporaryDirectory() as tmpdir: tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) @@ -378,6 +379,14 @@ def test_watcher( # extract tiffs check validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs) + if kwargs["extract_prof"]: + validators[0]( + os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs + ) + else: + assert not os.path.exists( + os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient" + ) # qc check validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs) diff --git a/tests/normalize_test.py b/tests/normalize_test.py index 4a163284..9d98966c 100644 --- a/tests/normalize_test.py +++ b/tests/normalize_test.py @@ -83,6 +83,11 @@ def test_write_mph_per_mass(mocker): assert set(output["mass"].values) == set(masses) assert np.all(output["pulse_height"].values == output["mass"].values * 2) + normalize.write_mph_per_mass( + base_dir=temp_dir, output_dir=out_dir, fov="fov1", masses=masses, proficient=True + ) + assert os.path.exists(os.path.join(out_dir, "fov1_pulse_heights_proficient.csv")) + @parametrize( "obj_func_name, num_params", @@ -152,16 +157,20 @@ def test_create_prediction_function(obj_func, num_params): @parametrize("warn_overwrite_test", [True, False]) def test_combine_run_metrics(metrics, warn_overwrite_test): with tempfile.TemporaryDirectory() as temp_dir: - for metric in metrics: + for metric in metrics["deficient"]: name, values_df = metric[0], pd.DataFrame(metric[1]) values_df.to_csv(os.path.join(temp_dir, name), index=False) + for metric in metrics["proficient"]: + name_prof, values_df_prof = metric[0], pd.DataFrame(metric[1]) + values_df_prof.to_csv(os.path.join(temp_dir, name_prof), index=False) + normalize.combine_run_metrics(temp_dir, "pulse_height") combined_data = pd.read_csv(os.path.join(temp_dir, "pulse_height_combined.csv")) assert np.array_equal(combined_data.columns, ["pulse_height", "mass", "fov"]) - assert len(combined_data) == len(metrics) * 10 + assert len(combined_data) == len(metrics["deficient"]) * 10 # check that previously generated combined file is removed with warning # NOTE: only if warn_overwrite turned on @@ -172,7 +181,7 @@ def test_combine_run_metrics(metrics, warn_overwrite_test): normalize.combine_run_metrics(temp_dir, "pulse_height", warn_overwrite_test) # check that files with different lengths raises error - name, bad_vals = metrics[0][0], pd.DataFrame(metrics[0][1]) + name, bad_vals = metrics["deficient"][0][0], pd.DataFrame(metrics["deficient"][0][1]) bad_vals = bad_vals.loc[0:5, :] bad_vals.to_csv(os.path.join(temp_dir, name), index=False) @@ -491,7 +500,7 @@ def test_create_fitted_pulse_heights_file(tmpdir, test_zeros, metrics): # create metric files pulse_dir = os.path.join(tmpdir, "pulse_heights") os.makedirs(pulse_dir) - for metric in metrics: + for metric in metrics["deficient"]: name, values_df = metric[0], pd.DataFrame(metric[1]) # if test_zeros, set first mass pulse height to 0 for every FOV @@ -500,6 +509,10 @@ def test_create_fitted_pulse_heights_file(tmpdir, test_zeros, metrics): values_df.to_csv(os.path.join(pulse_dir, name), index=False) + for metric in metrics["proficient"]: + name_prof, values_df_prof = metric[0], pd.DataFrame(metric[1]) + values_df_prof.to_csv(os.path.join(pulse_dir, name_prof), index=False) + panel = test_cases.panel fovs = natsort.natsorted(test_cases.fovs) @@ -633,10 +646,14 @@ def test_normalize_image_data(tmpdir, metrics): pulse_height_dir = os.path.join(tmpdir, "pulse_height_dir") os.makedirs(pulse_height_dir) - for metric in metrics: + for metric in metrics["deficient"]: name, values_df = metric[0], pd.DataFrame(metric[1]) values_df.to_csv(os.path.join(pulse_height_dir, name), index=False) + for metric in metrics["proficient"]: + name_prof, values_df_prof = metric[0], pd.DataFrame(metric[1]) + values_df_prof.to_csv(os.path.join(pulse_height_dir, name_prof), index=False) + # create directory with image data img_dir = os.path.join(tmpdir, "img_dir") os.makedirs(img_dir) diff --git a/tests/panel_utils_test.py b/tests/panel_utils_test.py index 62cffc6a..99adc658 100644 --- a/tests/panel_utils_test.py +++ b/tests/panel_utils_test.py @@ -9,6 +9,37 @@ from toffy import panel_utils +def test_modify_panel_ranges(): + # only Calprotectin's range should be adjusted + toffy_panel = pd.DataFrame( + { + "Mass": [69, 71, 89], + "Target": ["Calprotectin", "Chymase", "Mast Cell Tryptase"], + "Start": [68.7, 70.6, 89.3], + "Stop": [69, 71, 89], + } + ) + + toffy_panel_pos_offset = panel_utils.modify_panel_ranges( + toffy_panel, start_offset=0.3, stop_offset=0.3 + ) + + assert list(toffy_panel_pos_offset["Start"]) == [69, 70.6, 89.3] + assert list(toffy_panel_pos_offset["Stop"]) == [69.3, 71, 89] + + toffy_panel_neg_offset = panel_utils.modify_panel_ranges( + toffy_panel, start_offset=-0.3, stop_offset=-0.3 + ) + + assert list(toffy_panel_neg_offset["Start"]) == [68.4, 70.6, 89.3] + assert list(toffy_panel_neg_offset["Stop"]) == [68.7, 71, 89] + + toffy_panel_one_offset = panel_utils.modify_panel_ranges(toffy_panel, stop_offset=-0.3) + + assert list(toffy_panel_one_offset["Start"]) == [68.7, 70.6, 89.3] + assert list(toffy_panel_one_offset["Stop"]) == [68.7, 71, 89] + + def test_merge_duplicate_masses(): duplicate_panel = pd.DataFrame( { diff --git a/tests/utils/normalize_test_cases.py b/tests/utils/normalize_test_cases.py index 9e239b11..ed034973 100644 --- a/tests/utils/normalize_test_cases.py +++ b/tests/utils/normalize_test_cases.py @@ -96,14 +96,22 @@ def case_low_count_warn(self): class CombineRunMetricFiles: def case_default_metrics(self): - # create full directory of files + # create full directory of files, include proficient data which should be ignored metrics = [] + metrics_prof = [] for i in range(0, 4): metric_name = "pulse_heights_{}.csv".format(i) + metric_prof_name = "pulse_heights_{}_proficient.csv".format(i) metric_values = { "pulse_height": np.random.rand(10), "mass": masses, "fov": [fovs[i]] * 10, } + metric_prof_values = { + "pulse_height": np.random.rand(10), + "mass": masses, + "fov": [fovs[i]] * 10, + } metrics.append([metric_name, metric_values]) - return metrics + metrics_prof.append([metric_prof_name, metric_prof_values]) + return {"deficient": metrics, "proficient": metrics_prof} diff --git a/tests/utils/test_utils.py b/tests/utils/test_utils.py index 851d6cd4..1df5e12d 100644 --- a/tests/utils/test_utils.py +++ b/tests/utils/test_utils.py @@ -223,7 +223,12 @@ def mock_visualize_mph(mph_df, out_dir, return_plot=True, regression: bool = Fal class FovCallbackCases: def case_all_callbacks(self): panel_path = os.path.join(Path(__file__).parents[2], "data", "sample_panel.csv") - return FOV_CALLBACKS, {"panel": pd.read_csv(panel_path)} + return FOV_CALLBACKS, {"panel": pd.read_csv(panel_path), "extract_prof": True} + + def case_dont_extract_prof(self): + cbs, kwargs = self.case_all_callbacks() + kwargs["extract_prof"] = False + return cbs, kwargs def case_extract_only(self): cbs, kwargs = self.case_all_callbacks() @@ -266,13 +271,18 @@ def case_bad_callback(self): class RunCallbackCases: def case_default(self): panel_path = os.path.join(Path(__file__).parents[2], "data", "sample_panel.csv") - return RUN_CALLBACKS, None, {"panel": pd.read_csv(panel_path)} + return RUN_CALLBACKS, None, {"panel": pd.read_csv(panel_path), "extract_prof": True} def save_figure(self): cbs, ibs, kws = self.case_default() kws["save_dir"] = True return cbs, ibs, kws + def case_dont_extract_prof(self): + cbs, ibs, kws = self.case_default() + kws["extract_prof"] = False + return cbs, ibs, kws + def case_inter_callback(self): cbs, ibs, kws = self.case_default() ibs = list(cbs[:2]) @@ -396,6 +406,8 @@ def check_mph_dir_structure( def check_pulse_dir_structure(pulse_out_dir: str, point_names: List[str], bad_points: List[str]): """Checks pulse heights directory for minimum expected structure + Done for both proficient and deficient pulse height data + Args: pulse_out_dir (str): Folder containing pulse height files @@ -540,7 +552,8 @@ class WatcherCases: @parametrize(intensity=(False, True)) @parametrize(replace=(False, True)) - def case_default(self, intensity, replace): + @parametrize(extract_prof=(False, True)) + def case_default(self, intensity, replace, extract_prof): panel = pd.read_csv(os.path.join(Path(__file__).parents[2], "data", "sample_panel.csv")) validators = [ functools.partial( @@ -555,7 +568,12 @@ def case_default(self, intensity, replace): check_pulse_dir_structure, ] - kwargs = {"panel": panel, "intensities": intensity, "replace": replace} + kwargs = { + "panel": panel, + "extract_prof": extract_prof, + "intensities": intensity, + "replace": replace, + } return ( ["plot_qc_metrics", "plot_mph_metrics", "image_stitching"], @@ -569,8 +587,11 @@ def case_default(self, intensity, replace): @parametrize(intensity=(False, True)) @parametrize(replace=(False, True)) - def case_inter_callback(self, intensity, replace): - rcs, _, fcs, kwargs, validators, wsl, ed = self.case_default(intensity, replace) + @parametrize(extract_prof=(False, True)) + def case_inter_callback(self, intensity, replace, extract_prof): + rcs, _, fcs, kwargs, validators, wsl, ed = self.case_default( + intensity, replace, extract_prof + ) ics = rcs[:2] rcs = rcs[2:] @@ -578,10 +599,10 @@ def case_inter_callback(self, intensity, replace): @parametrize(watcher_start_lag=(4, 8, 12)) def case_watcher_lag(self, watcher_start_lag): - rcs, ics, fcs, kwargs, validators, _, ed = self.case_default(True, True) + rcs, ics, fcs, kwargs, validators, _, ed = self.case_default(True, True, True) return (rcs, ics, fcs, kwargs, validators, watcher_start_lag, ed) @parametrize(existing_data=((True, "Full"), (True, "Partial"), (False, None))) def case_existing_data(self, existing_data): - rcs, ics, fcs, kwargs, validators, wsl, _ = self.case_default(False, False) + rcs, ics, fcs, kwargs, validators, wsl, _ = self.case_default(False, False, True) return (rcs, ics, fcs, kwargs, validators, wsl, existing_data) diff --git a/tests/watcher_callbacks_test.py b/tests/watcher_callbacks_test.py index ff4713f0..30fe99aa 100644 --- a/tests/watcher_callbacks_test.py +++ b/tests/watcher_callbacks_test.py @@ -130,6 +130,10 @@ def test_build_callbacks(viz_mock, run_callbacks, inter_callbacks, kwargs, data_ icb(run_data) check_extraction_dir_structure(extracted_dir, point_names, [], ["SMA"]) + if kwargs["extract_prof"]: + check_extraction_dir_structure(extracted_dir + "_proficient", point_names, [], ["SMA"]) + else: + assert not os.path.exists(extracted_dir + "_proficient") check_qc_dir_structure(qc_dir, point_names, [], "save_dir" in kwargs) check_mph_dir_structure(qc_dir, plot_dir, point_names, [], combined=True) check_stitched_dir_structure(stitched_dir, ["SMA"])