cedanirs 0.0.1__tar.gz

cedanirs-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: cedanirs
+Version: 0.0.1
+Summary: A wrapper around cedalion for streamlined fNIRS preprocessing and analysis
+Author-email: Adam Emile Aske <adask2429@oslomet.no>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/adamaske/cedanirs
+Project-URL: Bug Tracker, https://github.com/adamaske/cedanirs/issues
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: xarray
+Requires-Dist: matplotlib
+Requires-Dist: cedalion
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+
+# cedanirs
+
+## What is Cedanirs?
+Cedanirs is a repository with reusable programs to process and analyze functional near-infrared spectroscopy (fNIRS) data. 
+
+## Modules
+- Preprocessing
+Input your .snirf file. Outputs preprocessed .snirf file.
+Motion correction. Temporal filtering. Normalization. 
+- Analysis
+GLM solvers. HRF estimation. DOT image reconstruction. 
+- Experiments
+Input standardaized experimental parameters, preprocess, analyze and report in a one swing.
+- 

cedanirs-0.0.1/README.md

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+# cedanirs
+
+## What is Cedanirs?
+Cedanirs is a repository with reusable programs to process and analyze functional near-infrared spectroscopy (fNIRS) data. 
+
+## Modules
+- Preprocessing
+Input your .snirf file. Outputs preprocessed .snirf file.
+Motion correction. Temporal filtering. Normalization. 
+- Analysis
+GLM solvers. HRF estimation. DOT image reconstruction. 
+- Experiments
+Input standardaized experimental parameters, preprocess, analyze and report in a one swing.
+- 

cedanirs-0.0.1/cedanirs/__init__.py

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+from .preprocessor import Preprocessor

cedanirs-0.0.1/cedanirs/preprocessor.py

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+from __future__ import annotations
+
+import xarray as xr
+import cedalion.io as io
+import cedalion.nirs.cw as cw
+import cedalion.sigproc.frequency as frequency
+
+
+class Preprocessor:
+    """Configurable preprocessing pipeline for cedalion fNIRS data.
+
+    Steps (in execution order):
+    1. Raw intensity -> Optical density
+    2. Motion correction (TDDR)
+    3. Optical density -> Haemoglobin (Beer-Lambert)
+    4. Bandpass temporal filtering
+
+    Usage::
+
+        pp = Preprocessor()
+        pp.set_bandpass(0.01, 0.2)
+        result = pp.apply(recording)
+
+    Or fluent::
+
+        result = Preprocessor().set_bandpass(0.01, 0.2).apply(recording)
+    """
+
+    def __init__(
+        self,
+        optical_density: bool = True,
+        motion_correction: bool = True,
+        hemoglobin: bool = True,
+        bandpass: bool = True,
+        bandpass_low: float = 0.01,
+        bandpass_high: float = 0.1,
+        dpf: float = 6.0,
+    ):
+        self.optical_density = optical_density
+        self.motion_correction = motion_correction
+        self.hemoglobin = hemoglobin
+        self.bandpass = bandpass
+        self.bandpass_low = bandpass_low
+        self.bandpass_high = bandpass_high
+        self.dpf = dpf
+
+    def set_optical_density(self, enabled: bool = True) -> "Preprocessor":
+        self.optical_density = enabled
+        return self
+
+    def set_motion_correction(self, enabled: bool = True) -> "Preprocessor":
+        self.motion_correction = enabled
+        return self
+
+    def set_hemoglobin(self, enabled: bool = True, dpf: float = 6.0) -> "Preprocessor":
+        self.hemoglobin = enabled
+        self.dpf = dpf
+        return self
+
+    def set_bandpass(self, low: float = 0.01, high: float = 0.1, enabled: bool = True) -> "Preprocessor":
+        self.bandpass = enabled
+        self.bandpass_low = low
+        self.bandpass_high = high
+        return self
+
+    def apply(self, recording):
+        """Apply the configured pipeline to a cedalion recording.
+
+        Parameters
+        ----------
+        recording:
+            A cedalion ``Recording`` or ``ContinuousData`` object.
+
+        Returns the processed recording.
+        """
+        raise NotImplementedError(
+            "Preprocessor.apply() is not yet implemented. "
+            "Wire cedalion calls here based on the loaded recording type."
+        )
+
+    def print(self) -> None:
+        print("Preprocessor Settings:")
+        print(f"  optical_density:          {self.optical_density}")
+        print(f"  motion_correction (TDDR): {self.motion_correction}")
+        print(f"  hemoglobin (Beer-Lambert):{self.hemoglobin} (dpf={self.dpf})")
+        print(f"  bandpass:                 {self.bandpass} ({self.bandpass_low}-{self.bandpass_high} Hz)")
+
+    def __repr__(self) -> str:
+        steps = []
+        if self.optical_density:
+            steps.append("OD")
+        if self.motion_correction:
+            steps.append("TDDR")
+        if self.hemoglobin:
+            steps.append("HbX")
+        if self.bandpass:
+            steps.append(f"BP({self.bandpass_low}-{self.bandpass_high})")
+        return f"Preprocessor([{' -> '.join(steps)}])"

cedanirs-0.0.1/cedanirs.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: cedanirs
+Version: 0.0.1
+Summary: A wrapper around cedalion for streamlined fNIRS preprocessing and analysis
+Author-email: Adam Emile Aske <adask2429@oslomet.no>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/adamaske/cedanirs
+Project-URL: Bug Tracker, https://github.com/adamaske/cedanirs/issues
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy
+Requires-Dist: xarray
+Requires-Dist: matplotlib
+Requires-Dist: cedalion
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+
+# cedanirs
+
+## What is Cedanirs?
+Cedanirs is a repository with reusable programs to process and analyze functional near-infrared spectroscopy (fNIRS) data. 
+
+## Modules
+- Preprocessing
+Input your .snirf file. Outputs preprocessed .snirf file.
+Motion correction. Temporal filtering. Normalization. 
+- Analysis
+GLM solvers. HRF estimation. DOT image reconstruction. 
+- Experiments
+Input standardaized experimental parameters, preprocess, analyze and report in a one swing.
+- 

cedanirs-0.0.1/cedanirs.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+cedanirs/__init__.py
+cedanirs/preprocessor.py
+cedanirs.egg-info/PKG-INFO
+cedanirs.egg-info/SOURCES.txt
+cedanirs.egg-info/dependency_links.txt
+cedanirs.egg-info/requires.txt
+cedanirs.egg-info/top_level.txt
+tests/test_preprocessor.py

cedanirs-0.0.1/cedanirs.egg-info/dependency_links.txt

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+

cedanirs-0.0.1/cedanirs.egg-info/requires.txt

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+numpy
+xarray
+matplotlib
+cedalion
+
+[dev]
+pytest
+black
+flake8

cedanirs-0.0.1/cedanirs.egg-info/top_level.txt

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+cedanirs

cedanirs-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cedanirs"
+version = "0.0.1"
+description = "A wrapper around cedalion for streamlined fNIRS preprocessing and analysis"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.10"
+authors = [{ name = "Adam Emile Aske", email = "adask2429@oslomet.no" }]
+classifiers = [
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Operating System :: OS Independent",
+  "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = ["numpy", "xarray", "matplotlib", "cedalion"]
+
+[project.urls]
+Homepage = "https://github.com/adamaske/cedanirs"
+"Bug Tracker" = "https://github.com/adamaske/cedanirs/issues"
+
+[project.optional-dependencies]
+dev = ["pytest", "black", "flake8"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["cedanirs*"]

cedanirs-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

cedanirs-0.0.1/tests/test_preprocessor.py

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+import pytest
+from cedanirs import Preprocessor
+
+
+def test_preprocessor_defaults():
+    pp = Preprocessor()
+    assert pp.optical_density is True
+    assert pp.motion_correction is True
+    assert pp.hemoglobin is True
+    assert pp.bandpass is True
+    assert pp.bandpass_low == 0.01
+    assert pp.bandpass_high == 0.1
+
+
+def test_preprocessor_fluent_builder():
+    pp = Preprocessor().set_bandpass(0.02, 0.3).set_motion_correction(False)
+    assert pp.bandpass_low == 0.02
+    assert pp.bandpass_high == 0.3
+    assert pp.motion_correction is False
+
+
+def test_preprocessor_repr():
+    pp = Preprocessor()
+    r = repr(pp)
+    assert "OD" in r
+    assert "TDDR" in r
+    assert "HbX" in r
+    assert "BP" in r