From a7cd9e206cde1dbc433a531b501f46756b2764aa Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 10:38:17 -0500 Subject: [PATCH 01/40] feat: add functions for correlation matrix calculations and subsetting --- src/readii/analyze/__init__.py | 10 +++ src/readii/analyze/correlation.py | 144 ++++++++++++++++++++++++++++++ 2 files changed, 154 insertions(+) create mode 100644 src/readii/analyze/__init__.py create mode 100644 src/readii/analyze/correlation.py diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py new file mode 100644 index 0000000..cfe1f83 --- /dev/null +++ b/src/readii/analyze/__init__.py @@ -0,0 +1,10 @@ +""" Module to perform analysis on READII outputs """ + +from .correlation import getFeatureCorrelations, getVerticalSelfCorrelations, getHorizontalSelfCorrelations, getCrossCorrelationMatrix + +__all__ = [ + 'getFeatureCorrelations', + 'getVerticalSelfCorrelations', + 'getHorizontalSelfCorrelations', + 'getCrossCorrelationMatrix' +] \ No newline at end of file diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py new file mode 100644 index 0000000..ec4af57 --- /dev/null +++ b/src/readii/analyze/correlation.py @@ -0,0 +1,144 @@ +import pandas as pd + + +def getFeatureCorrelations(vertical_features:pd.DataFrame, + horizontal_features:pd.DataFrame, + method:str = "pearson", + vertical_feature_name:str = '_vertical', + horizontal_feature_name:str = '_horizontal'): + """ Function to calculate correlation between two sets of features. + + Parameters + ---------- + vertical_features : pd.DataFrame + Dataframe containing features to calculate correlations with. Index must be the same as the index of the horizontal_features dataframe. + horizontal_features : pd.DataFrame + Dataframe containing features to calculate correlations with. Index must be the same as the index of the vertical_features dataframe. + method : str + Method to use for calculating correlations. Default is "pearson". + vertical_feature_name : str + Name of the vertical features to use as suffix in correlation dataframe. Default is blank "". + horizontal_feature_name : str + Name of the horizontal features to use as suffix in correlation dataframe. Default is blank "". + + Returns + ------- + correlation_matrix : pd.DataFrame + Dataframe containing correlation values. + """ + # Check that features are dataframes + if not isinstance(vertical_features, pd.DataFrame): + raise TypeError("vertical_features must be a pandas DataFrame") + if not isinstance(horizontal_features, pd.DataFrame): + raise TypeError("horizontal_features must be a pandas DataFrame") + + + if method not in ["pearson", "spearman", "kendall"]: + raise ValueError("Correlation method must be one of 'pearson', 'spearman', or 'kendall'.") + + if not vertical_features.index.equals(horizontal_features.index): + raise ValueError("Vertical and horizontal features must have the same index to calculate correlation. Set the index to the intersection of patient IDs.") + + # Add _ to beginnging of feature names if they don't start with _ so they can be used as suffixes + if not vertical_feature_name.startswith("_"): vertical_feature_name = f"_{vertical_feature_name}" + if not horizontal_feature_name.startswith("_"): horizontal_feature_name = f"_{horizontal_feature_name}" + + # Join the features into one dataframe + # Use inner join to keep only the rows that have a value in both vertical and horizontal features + features_to_correlate = vertical_features.join(horizontal_features, + how='inner', + lsuffix=vertical_feature_name, + rsuffix=horizontal_feature_name) + + try: + # Calculate correlation between vertical features and horizontal features + correlation_matrix = features_to_correlate.corr(method=method) + except Exception as e: + raise ValueError(f"Error calculating correlation matrix: {e}") + + return correlation_matrix + + + +def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, + num_vertical_features:int): + """ Function to get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. + + Parameters + ---------- + correlation_matrix : pd.DataFrame + Dataframe containing the correlation matrix to get the vertical self correlations from. + num_vertical_features : int + Number of vertical features in the correlation matrix. + + Returns + ------- + pd.DataFrame + Dataframe containing the vertical self correlations from the correlation matrix. + """ + if num_vertical_features > correlation_matrix.shape[0]: + raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + + if num_vertical_features > correlation_matrix.shape[1]: + raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + + # Get the correlation matrix for vertical vs vertical - this is the top left corner of the matrix + return correlation_matrix.iloc[0:num_vertical_features, 0:num_vertical_features] + + + +def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, + num_horizontal_features:int): + """ Function to get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. + + Parameters + ---------- + correlation_matrix : pd.DataFrame + Dataframe containing the correlation matrix to get the horizontal self correlations from. + num_horizontal_features : int + Number of horizontal features in the correlation matrix. + + Returns + ------- + pd.DataFrame + Dataframe containing the horizontal self correlations from the correlation matrix. + """ + + if num_horizontal_features > correlation_matrix.shape[0]: + raise ValueError(f"Number of horizontal features ({num_horizontal_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + + if num_horizontal_features > correlation_matrix.shape[1]: + raise ValueError(f"Number of horizontal features ({num_horizontal_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + + # Get the index of the start of the horizontal correlations + start_of_horizontal_correlations = len(correlation_matrix.columns) - num_horizontal_features + + # Get the correlation matrix for horizontal vs horizontal - this is the bottom right corner of the matrix + return correlation_matrix.iloc[start_of_horizontal_correlations:, start_of_horizontal_correlations:] + + + +def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, + num_vertical_features:int): + """ Function to get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. + + Parameters + ---------- + correlation_matrix : pd.DataFrame + Dataframe containing the correlation matrix to get the cross correlation matrix subsection from. + num_vertical_features : int + Number of vertical features in the correlation matrix. + + Returns + ------- + pd.DataFrame + Dataframe containing the cross correlations from the correlation matrix. + """ + + if num_vertical_features > correlation_matrix.shape[0]: + raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + + if num_vertical_features > correlation_matrix.shape[1]: + raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + + return correlation_matrix.iloc[0:num_vertical_features, num_vertical_features:] \ No newline at end of file From bceafa424c4189dec41ae74ce4ecf8e1a6f911a6 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 10:39:52 -0500 Subject: [PATCH 02/40] style: change feature name if statements to be multi-line --- src/readii/analyze/correlation.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index ec4af57..e3c76eb 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -40,8 +40,10 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, raise ValueError("Vertical and horizontal features must have the same index to calculate correlation. Set the index to the intersection of patient IDs.") # Add _ to beginnging of feature names if they don't start with _ so they can be used as suffixes - if not vertical_feature_name.startswith("_"): vertical_feature_name = f"_{vertical_feature_name}" - if not horizontal_feature_name.startswith("_"): horizontal_feature_name = f"_{horizontal_feature_name}" + if not vertical_feature_name.startswith("_"): + vertical_feature_name = f"_{vertical_feature_name}" + if not horizontal_feature_name.startswith("_"): + horizontal_feature_name = f"_{horizontal_feature_name}" # Join the features into one dataframe # Use inner join to keep only the rows that have a value in both vertical and horizontal features From dc60e19cc187c6d47561a5a22b1fab447c9dd28e Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 10:46:32 -0500 Subject: [PATCH 03/40] build: updated pixi lock file --- pixi.lock | 244 +----------------------------------------------------- 1 file changed, 2 insertions(+), 242 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0461c8e..469671c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1783,8 +1783,6 @@ packages: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726 md5: d7c89558ba9fa0495403155b64376d81 - arch: x86_64 - platform: linux license: None purls: [] size: 2562 @@ -1798,8 +1796,6 @@ packages: - libgomp >=7.5.0 constrains: - openmp_impl 9999 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -1984,8 +1980,6 @@ packages: - libgcc >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -2001,8 +1995,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -2201,8 +2193,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - libbrotlicommon 1.1.0 hb9d3cd8_2 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -2220,8 +2210,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - libbrotlicommon 1.1.0 hd74edd7_2 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -2234,8 +2222,6 @@ packages: depends: - __glibc >=2.17,<3.0.a0 - libgcc-ng >=12 - arch: x86_64 - platform: linux license: bzip2-1.0.6 license_family: BSD purls: [] @@ -2246,8 +2232,6 @@ packages: md5: fc6948412dbbbe9a4c9ddbbcfe0a79ab depends: - __osx >=11.0 - arch: arm64 - platform: osx license: bzip2-1.0.6 license_family: BSD purls: [] @@ -2256,8 +2240,6 @@ packages: - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda sha256: afee721baa6d988e27fef1832f68d6f32ac8cc99cdf6015732224c2841a09cea md5: c27d1c142233b5bc9ca570c6e2e0c244 - arch: x86_64 - platform: linux license: ISC purls: [] size: 159003 @@ -2265,8 +2247,6 @@ packages: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ca-certificates-2024.8.30-hf0a4a13_0.conda sha256: 2db1733f4b644575dbbdd7994a8f338e6ef937f5ebdb74acd557e9dda0211709 md5: 40dec13fd8348dbe303e57be74bd3d35 - 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platform: linux license: X11 AND BSD-3-Clause purls: [] size: 889086 @@ -5135,8 +5013,6 @@ packages: md5: cb2b0ea909b97b3d70cd3921d1445e1a depends: - __osx >=11.0 - arch: arm64 - platform: osx license: X11 AND BSD-3-Clause purls: [] size: 802321 @@ -5248,8 +5124,6 @@ packages: - __glibc >=2.17,<3.0.a0 - ca-certificates - libgcc >=13 - arch: x86_64 - platform: linux license: Apache-2.0 license_family: Apache purls: [] @@ -5261,8 +5135,6 @@ packages: depends: - __osx >=11.0 - ca-certificates - arch: arm64 - platform: osx license: Apache-2.0 license_family: Apache purls: [] @@ -5275,8 +5147,6 @@ packages: - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - typing-extensions >=4.10 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: @@ -5291,8 +5161,6 @@ packages: - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - typing-extensions >=4.10 - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: @@ -5934,8 +5802,6 @@ packages: - bzip2 >=1.0.8,<2.0a0 - libgcc-ng >=12 - libzlib >=1.3.1,<2.0a0 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -6256,8 +6122,6 @@ packages: - libgcc >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: Apache-2.0 license_family: APACHE purls: @@ -6272,8 +6136,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: Apache-2.0 license_family: APACHE purls: @@ -6288,8 +6150,6 @@ packages: - libgcc >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: @@ -6304,8 +6164,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: @@ -6381,8 +6239,6 @@ packages: - typing-extensions >=4.6.0,!=4.7.0 constrains: - __glibc >=2.17 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -6400,8 +6256,6 @@ packages: - typing-extensions >=4.6.0,!=4.7.0 constrains: - __osx >=11.0 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -6501,8 +6355,6 @@ packages: - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - setuptools - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -6519,8 +6371,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -6642,8 +6492,6 @@ packages: - tzdata constrains: - python_abi 3.10.* *_cp310 - arch: x86_64 - platform: linux license: Python-2.0 purls: [] size: 25199631 @@ -6672,8 +6520,6 @@ packages: - tzdata constrains: - python_abi 3.11.* *_cp311 - arch: x86_64 - platform: linux license: Python-2.0 purls: [] size: 30624804 @@ -6702,8 +6548,6 @@ packages: - tzdata constrains: - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: Python-2.0 purls: [] size: 31565686 @@ -6726,8 +6570,6 @@ packages: - tzdata constrains: - python_abi 3.10.* *_cp310 - arch: arm64 - platform: osx license: Python-2.0 purls: [] size: 12372048 @@ -6751,8 +6593,6 @@ packages: - tzdata constrains: - python_abi 3.11.* *_cp311 - arch: arm64 - platform: osx license: Python-2.0 purls: [] size: 14647146 @@ -6776,8 +6616,6 @@ packages: - tzdata constrains: - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: Python-2.0 purls: [] size: 12998673 @@ -6866,8 +6704,6 @@ packages: md5: 2921c34715e74b3587b4cff4d36844f9 constrains: - python 3.10.* *_cpython - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -6879,8 +6715,6 @@ packages: md5: 139a8d40c8a2f430df31048949e450de constrains: - python 3.11.* *_cpython - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -6892,8 +6726,6 @@ packages: md5: 0424ae29b104430108f5218a66db7260 constrains: - python 3.12.* *_cpython - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -6905,8 +6737,6 @@ packages: md5: e33836c9096802b29d28981765becbee constrains: - python 3.10.* *_cpython - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: [] @@ -6918,8 +6748,6 @@ packages: md5: 3b855e3734344134cb56c410f729c340 constrains: - python 3.11.* *_cpython - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: [] @@ -6931,8 +6759,6 @@ packages: md5: b76f9b1c862128e56ac7aa8cd2333de9 constrains: - python 3.12.* *_cpython - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: [] @@ -7040,8 +6866,6 @@ packages: - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - yaml >=0.2.5,<0.3.0a0 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -7057,8 +6881,6 @@ packages: - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - yaml >=0.2.5,<0.3.0a0 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -7088,8 +6910,6 @@ packages: - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - zeromq >=4.3.5,<4.4.0a0 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: @@ -7107,8 +6927,6 @@ packages: - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - zeromq >=4.3.5,<4.4.0a0 - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: @@ -7117,8 +6935,8 @@ packages: timestamp: 1728642457661 - pypi: . name: readii - version: 1.22.0 - sha256: 17cfade190918fb8a7edbe1067b2a0e53170ee5b065416cdfeffa35fe641d037 + version: 1.25.0 + sha256: 075ffd6627bff9721d281a4715fb8fb3dedf9bb082450f18f5872d24f6592162 requires_dist: - simpleitk>=2.3.1 - matplotlib>=3.9.2,<4 @@ -7134,8 +6952,6 @@ packages: depends: - libgcc-ng >=12 - ncurses >=6.3,<7.0a0 - arch: x86_64 - platform: linux license: GPL-3.0-only license_family: GPL purls: [] @@ -7146,8 +6962,6 @@ packages: md5: 8cbb776a2f641b943d413b3e19df71f4 depends: - ncurses >=6.3,<7.0a0 - arch: arm64 - platform: osx license: GPL-3.0-only license_family: GPL purls: [] @@ -7174,8 +6988,6 @@ packages: - libgcc >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: Python-2.0 license_family: PSF purls: @@ -7190,8 +7002,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: Python-2.0 license_family: PSF purls: @@ -7284,8 +7094,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - __glibc >=2.17 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -7302,8 +7110,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - __osx >=11.0 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -7361,8 +7167,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - __glibc >=2.17 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -7380,8 +7184,6 @@ packages: - python_abi 3.12.* *_cp312 constrains: - __osx >=11.0 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -8425,8 +8227,6 @@ packages: - jeepney >=0.6 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: @@ -8906,8 +8706,6 @@ packages: depends: - libgcc-ng >=12 - libzlib >=1.2.13,<2.0.0a0 - arch: x86_64 - platform: linux license: TCL license_family: BSD purls: [] @@ -8918,8 +8716,6 @@ packages: md5: b50a57ba89c32b62428b71a875291c9b depends: - libzlib >=1.2.13,<2.0.0a0 - arch: arm64 - platform: osx license: TCL license_family: BSD purls: [] @@ -8977,8 +8773,6 @@ packages: - libgcc >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: Apache-2.0 license_family: Apache purls: @@ -8993,8 +8787,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: Apache-2.0 license_family: Apache purls: @@ -9109,8 +8901,6 @@ packages: - libstdcxx >=13 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: @@ -9127,8 +8917,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: @@ -9182,8 +8970,6 @@ packages: - libstdcxx >=13 constrains: - __glibc >=2.17 - arch: x86_64 - platform: linux license: Apache-2.0 OR MIT purls: [] size: 10382046 @@ -9196,8 +8982,6 @@ packages: - libcxx >=18 constrains: - __osx >=11.0 - arch: arm64 - platform: osx license: Apache-2.0 OR MIT purls: [] size: 10186932 @@ -9234,8 +9018,6 @@ packages: - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - pyyaml >=3.10 - arch: x86_64 - platform: linux license: Apache-2.0 license_family: APACHE purls: @@ -9251,8 +9033,6 @@ packages: - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - pyyaml >=3.10 - arch: arm64 - platform: osx license: Apache-2.0 license_family: APACHE purls: @@ -9331,8 +9111,6 @@ packages: md5: 4cb3ad778ec2d5a7acbdf254eb1c42ae depends: - libgcc-ng >=9.4.0 - arch: x86_64 - platform: linux license: MIT license_family: MIT purls: [] @@ -9341,8 +9119,6 @@ packages: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h3422bc3_2.tar.bz2 sha256: 93181a04ba8cfecfdfb162fc958436d868cc37db504c58078eab4c1a3e57fbb7 md5: 4bb3f014845110883a3c5ee811fd84b4 - arch: arm64 - platform: osx license: MIT license_family: MIT purls: [] @@ -9413,8 +9189,6 @@ packages: - propcache >=0.2.1 - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 - arch: x86_64 - platform: linux license: Apache-2.0 license_family: Apache purls: @@ -9432,8 +9206,6 @@ packages: - python >=3.12,<3.13.0a0 - python >=3.12,<3.13.0a0 *_cpython - python_abi 3.12.* *_cp312 - arch: arm64 - platform: osx license: Apache-2.0 license_family: Apache purls: @@ -9449,8 +9221,6 @@ packages: - libgcc >=13 - libsodium >=1.0.20,<1.0.21.0a0 - libstdcxx >=13 - arch: x86_64 - platform: linux license: MPL-2.0 license_family: MOZILLA purls: [] @@ -9464,8 +9234,6 @@ packages: - krb5 >=1.21.3,<1.22.0a0 - libcxx >=18 - libsodium >=1.0.20,<1.0.21.0a0 - arch: arm64 - platform: osx license: MPL-2.0 license_family: MOZILLA purls: [] @@ -9493,8 +9261,6 @@ packages: - python_abi 3.12.* *_cp312 - zstd >=1.5.6,<1.5.7.0a0 - zstd >=1.5.6,<1.6.0a0 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: @@ -9512,8 +9278,6 @@ packages: - python_abi 3.12.* *_cp312 - zstd >=1.5.6,<1.5.7.0a0 - zstd >=1.5.6,<1.6.0a0 - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: @@ -9527,8 +9291,6 @@ packages: - libgcc-ng >=12 - libstdcxx-ng >=12 - libzlib >=1.2.13,<2.0.0a0 - arch: x86_64 - platform: linux license: BSD-3-Clause license_family: BSD purls: [] @@ -9540,8 +9302,6 @@ packages: depends: - __osx >=11.0 - libzlib >=1.2.13,<2.0.0a0 - arch: arm64 - platform: osx license: BSD-3-Clause license_family: BSD purls: [] From c426006ad35f1423173732243656cd48487c0a8b Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 10:54:07 -0500 Subject: [PATCH 04/40] feat: add readii logger for errors and exceptions --- src/readii/analyze/correlation.py | 47 ++++++++++++++++++++++--------- 1 file changed, 34 insertions(+), 13 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index e3c76eb..6381ce9 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -1,5 +1,5 @@ import pandas as pd - +from readii.utils import logger def getFeatureCorrelations(vertical_features:pd.DataFrame, horizontal_features:pd.DataFrame, @@ -28,16 +28,23 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, """ # Check that features are dataframes if not isinstance(vertical_features, pd.DataFrame): - raise TypeError("vertical_features must be a pandas DataFrame") + msg = "vertical_features must be a pandas DataFrame" + logger.exception(msg) + raise TypeError() if not isinstance(horizontal_features, pd.DataFrame): - raise TypeError("horizontal_features must be a pandas DataFrame") - + msg = "horizontal_features must be a pandas DataFrame" + logger.exception(msg) + raise TypeError() if method not in ["pearson", "spearman", "kendall"]: - raise ValueError("Correlation method must be one of 'pearson', 'spearman', or 'kendall'.") + msg = "Correlation method must be one of 'pearson', 'spearman', or 'kendall'." + logger.exception(msg) + raise ValueError() if not vertical_features.index.equals(horizontal_features.index): - raise ValueError("Vertical and horizontal features must have the same index to calculate correlation. Set the index to the intersection of patient IDs.") + msg = "Vertical and horizontal features must have the same index to calculate correlation. Set the index to the intersection of patient IDs." + logger.exception(msg) + raise ValueError() # Add _ to beginnging of feature names if they don't start with _ so they can be used as suffixes if not vertical_feature_name.startswith("_"): @@ -56,7 +63,9 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, # Calculate correlation between vertical features and horizontal features correlation_matrix = features_to_correlate.corr(method=method) except Exception as e: - raise ValueError(f"Error calculating correlation matrix: {e}") + msg = f"Error calculating correlation matrix: {e}" + logger.exception(msg) + raise e return correlation_matrix @@ -79,10 +88,14 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, Dataframe containing the vertical self correlations from the correlation matrix. """ if num_vertical_features > correlation_matrix.shape[0]: - raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." + logger.exception(msg) + raise ValueError() if num_vertical_features > correlation_matrix.shape[1]: - raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." + logger.exception(msg) + raise ValueError() # Get the correlation matrix for vertical vs vertical - this is the top left corner of the matrix return correlation_matrix.iloc[0:num_vertical_features, 0:num_vertical_features] @@ -107,10 +120,14 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, """ if num_horizontal_features > correlation_matrix.shape[0]: - raise ValueError(f"Number of horizontal features ({num_horizontal_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + msg = f"Number of horizontal features ({num_horizontal_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." + logger.exception(msg) + raise ValueError() if num_horizontal_features > correlation_matrix.shape[1]: - raise ValueError(f"Number of horizontal features ({num_horizontal_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + msg = f"Number of horizontal features ({num_horizontal_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." + logger.exception(msg) + raise ValueError() # Get the index of the start of the horizontal correlations start_of_horizontal_correlations = len(correlation_matrix.columns) - num_horizontal_features @@ -138,9 +155,13 @@ def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, """ if num_vertical_features > correlation_matrix.shape[0]: - raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]}).") + msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." + logger.exception(msg) + raise ValueError() if num_vertical_features > correlation_matrix.shape[1]: - raise ValueError(f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]}).") + msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." + logger.exception(msg) + raise ValueError() return correlation_matrix.iloc[0:num_vertical_features, num_vertical_features:] \ No newline at end of file From b0bd53cfb03b2489a54e67d62a63855fb84b0ba8 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 10:54:49 -0500 Subject: [PATCH 05/40] test: add testing for getFeatureCorrelations --- tests/analyze/test_correlation.py | 114 ++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) create mode 100644 tests/analyze/test_correlation.py diff --git a/tests/analyze/test_correlation.py b/tests/analyze/test_correlation.py new file mode 100644 index 0000000..e614401 --- /dev/null +++ b/tests/analyze/test_correlation.py @@ -0,0 +1,114 @@ +from readii.analyze.correlation import ( + getFeatureCorrelations +) + +import pytest +import pandas as pd +import numpy as np + +@pytest.fixture +def random_features(): + # Create a 10x10 matrix with random float values between 0 and 1 + random_matrix = np.random.default_rng(seed=10).random((10,10)) + # Convert to dataframe and name the columns feature1, feature2, etc. + return pd.DataFrame(random_matrix, columns=[f"feature_{i+1}" for i in range(10)]) + +@pytest.mark.parametrize( + "correlation_method", + [ + "pearson", + "spearman", + "kendall" + ] +) +def test_methods_getFeatureCorrelation(correlation_method, random_features): + """Test getting correlation matrix for a set of random_features with pearson and spearman correlation methods""" + + features_to_corr = random_features.join(random_features, how='inner', lsuffix='_vertical', rsuffix='_horizontal') + expected = features_to_corr.corr(method=correlation_method) + + actual = getFeatureCorrelations(vertical_features = random_features, + horizontal_features = random_features, + method = correlation_method + ) + assert isinstance(actual, pd.DataFrame), \ + "Wrong return type, expect a pandas DataFrame" + assert actual.shape[0] == 2*random_features.shape[1], \ + "Wrong return size, should be double the number of input features" + assert actual.equals(expected), \ + f"{correlation_method} correlation values are incorrect for the input features" + + +def test_defaults_getFeatureCorrelations(random_features): + """Test the default argument behaviours of getFeatureCorrelations. Should be a Pearson correlation matrix with _vertical and _horizontal suffixes on the feature names""" + features_to_corr = random_features.join(random_features, how='inner', lsuffix='_vertical', rsuffix='_horizontal') + expected = features_to_corr.corr(method="pearson") + + actual = getFeatureCorrelations(vertical_features = random_features, + horizontal_features = random_features) + assert isinstance(actual, pd.DataFrame), \ + "Wrong return type, expect a pandas DataFrame" + assert actual.shape[0] == 2*random_features.shape[1], \ + "Wrong return size, should be double the number of the input features" + assert actual.equals(expected), \ + "Pearson correlation values are incorrect for the input features" + assert actual.columns.equals(expected.columns), \ + "Column names are incorrect. Should be the input features with _vertical and _horizontal suffixes" + + +@pytest.mark.parametrize( + "correlation_method", + [ + "random", + "" + ] +) +def test_wrongMethod_getFeatureCorrelations(random_features, correlation_method): + """Check ValueError is raised when incorrect correlation method is passed""" + with pytest.raises(ValueError): + getFeatureCorrelations(vertical_features = random_features, + horizontal_features = random_features, + method = correlation_method + ) + +@pytest.mark.parametrize( + "wrong_features", + [ + np.random.default_rng(seed=10).random((10,10)), + "Just a string", + {"feat1": 34, "feat2": 10000, "feat3": 3.141592} + ] +) +def test_wrongFeatures_getFeatureCorrelations(random_features, wrong_features): + """Check ValueError is raised when incorrect features are passed""" + with pytest.raises(TypeError): + getFeatureCorrelations(vertical_features = random_features, + horizontal_features = wrong_features, + method = "pearson" + ) + with pytest.raises(TypeError): + getFeatureCorrelations(vertical_features = wrong_features, + horizontal_features = random_features, + method = "pearson" + ) + +@pytest.mark.parametrize( + "vertical_feature_name, horizontal_feature_name, expected_vertical, expected_horizontal", + [ + ("type_A", "type_B", [f"feature_{i+1}_type_A" for i in range(10)], [f"feature_{i+1}_type_B" for i in range(10)]), + ("_type_C", "_type_D", [f"feature_{i+1}_type_C" for i in range(10)], [f"feature_{i+1}_type_D" for i in range(10)]), + ] +) +def test_featureNames_getFeatureCorrelations(random_features, vertical_feature_name, horizontal_feature_name, expected_vertical, expected_horizontal): + """ Check that feature names with and without _ prefix are handled correctly""" + + actual = getFeatureCorrelations(vertical_features=random_features, + horizontal_features=random_features, + vertical_feature_name=vertical_feature_name, + horizontal_feature_name=horizontal_feature_name) + + assert list(actual.columns) == expected_vertical + expected_horizontal, \ + "Column names are incorrect, check underscore prefix handling when adding the vertical and horizontal feature names. Should be [feature]_vertical_feature_name and [feature]_horizontal_feature_name." + assert list(actual.index) == expected_vertical + expected_horizontal, \ + "Index values are incorrect, check underscore prefix handling when adding the vertical and horizontal feature names. Should be [feature]_vertical_feature_name and [feature]_horizontal_feature_name." + \ No newline at end of file From 971345538a79ae3f44804b460857ee21d1c8c50d Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 11:03:35 -0500 Subject: [PATCH 06/40] build: add seaborn for plotting Had to specify numpy due to dependency clash between seaborn and med-imagetools --- pixi.lock | 4260 +++++++++++++++++++++++++++++------------------- pyproject.toml | 2 + 2 files changed, 2546 insertions(+), 1716 deletions(-) diff --git a/pixi.lock b/pixi.lock index 469671c..eeebb54 100644 --- a/pixi.lock +++ b/pixi.lock @@ -9,64 +9,103 @@ environments: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb9d3cd8_2.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb9d3cd8_2.conda - 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"seaborn>=0.13.2,<0.14" + "seaborn>=0.13.2,<0.14", + "pandas>=2.2.3,<3" ] requires-python = ">=3.10, <3.13" From f690a46a615689a682bfa48bbd4d1716a910a94b Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 11:56:56 -0500 Subject: [PATCH 08/40] feat: add function to plot a correlation matrix as a seaborn heatmap --- src/readii/analyze/plot_correlation.py | 92 ++++++++++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 src/readii/analyze/plot_correlation.py diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py new file mode 100644 index 0000000..fa94136 --- /dev/null +++ b/src/readii/analyze/plot_correlation.py @@ -0,0 +1,92 @@ +from typing import Optional +import matplotlib.pyplot as plt +import seaborn as sns +import numpy as np +import pandas as pd + +from readii.utils import logger + +def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, + diagonal:bool = False, + triangle:Optional[str] = "lower", + cmap:str = "nipy_spectral", + xlabel:str = "", + ylabel:Optional[str] = "", + title:Optional[str] = "", + subtitle:Optional[str] = "", + show_tick_labels:bool = False + ): + """Function to plot a correlation heatmap. + + Parameters + ---------- + correlation_matrix_df : pd.DataFrame + Dataframe containing the correlation matrix to plot. + diagonal : bool, optional + Whether to only plot half of the matrix. The default is False. + triangle : str, optional + Which triangle half of the matrixto plot. The default is "lower". + xlabel : str, optional + Label for the x-axis. The default is "". + ylabel : str, optional + Label for the y-axis. The default is "". + title : str, optional + Title for the plot. The default is "". + subtitle : str, optional + Subtitle for the plot. The default is "". + show_tick_labels : bool, optional + Whether to show the tick labels on the x and y axes. These would be the feature names. The default is False. + + Returns + ------- + corr_fig : matplotlib.pyplot.figure + Figure object containing a Seaborn heatmap. + """ + + if diagonal: + logger.debug(f"Creating {triangle} traingle mask for diagonal correlation plot.") + # Set up mask for hiding half the matrix in the plot + if triangle == "lower": + # Mask out the upper right triangle half of the matrix + mask = np.triu(correlation_matrix_df) + elif triangle == "upper": + # Mask out the lower left triangle half of the matrix + mask = np.tril(correlation_matrix_df) + else: + msg = f"If diagonal is True, triangle must be either 'lower' or 'upper'. Got {triangle}." + logger.exception(msg) + raise ValueError() + else: + logger.debug("Creating full square correlation matrix plot.") + # The entire correlation matrix will be visisble in the plot + mask = None + + # Set a default title if one is not provided + if not title: + title = "Correlation Heatmap" + + # Set up figure and axes for the plot + corr_fig, corr_ax = plt.subplots() + + # Plot the correlation matrix + corr_ax = sns.heatmap(correlation_matrix_df, + mask = mask, + cmap=cmap, + vmin=-1.0, + vmax=1.0) + + if not show_tick_labels: + # Remove the individual feature names from the axes + corr_ax.set_xticklabels(labels=[]) + corr_ax.set_yticklabels(labels=[]) + + # Set axis labels + corr_ax.set_xlabel(xlabel) + corr_ax.set_ylabel(ylabel) + + # Set title and subtitle + # Suptitle is the super title, which will be above the title + plt.title(subtitle, fontsize=12) + plt.suptitle(title, fontsize=14) + + return corr_fig \ No newline at end of file From 6370597f5e8ca42944aa6a6eb0284481dc208ff6 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 12:02:27 -0500 Subject: [PATCH 09/40] feat: add function for plotting correlation distribution as a histogram --- src/readii/analyze/plot_correlation.py | 80 +++++++++++++++++++++++++- 1 file changed, 79 insertions(+), 1 deletion(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index fa94136..78cbc2a 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -3,6 +3,7 @@ import seaborn as sns import numpy as np import pandas as pd +from scipy.linalg import issymmetric from readii.utils import logger @@ -89,4 +90,81 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, plt.title(subtitle, fontsize=12) plt.suptitle(title, fontsize=14) - return corr_fig \ No newline at end of file + return corr_fig + + + +def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, + num_bins:int = 100, + xlabel:Optional[str] = "Correlations", + ylabel:Optional[str] = "Frequency", + y_lower_bound:int = 0, + y_upper_bound:Optional[int] = None, + title:Optional[str] = "Distribution of Correlations for Features", + subtitle:Optional[str] = "", + ): + """ Function to plot a distribution of correlation values for a correlation matrix. + + Parameters + ---------- + correlation_matrix : pd.DataFrame + Dataframe containing the correlation matrix to plot. + num_bins : int, optional + Number of bins to use for the distribution plot. The default is 100. + xlabel : str, optional + Label for the x-axis. The default is "Correlations". + ylabel : str, optional + Label for the y-axis. The default is "Frequency". + y_lower_bound : int, optional + Lower bound for the y-axis of the distribution plot. The default is 0. + y_upper_bound : int, optional + Upper bound for the y-axis of the distribution plot. The default is None. + title : str, optional + Title for the plot. The default is "Distribution of Correlations for Features". + subtitle : str, optional + Subtitle for the plot. The default is "". + + Returns + ------- + dist_fig : plt.Figure + Figure object containing the histogram of correlation values. + bin_values : np.ndarray or list of arrays + Numpy array containing the values in each bin for the histogram. + bin_edges : np.ndarray + Numpy array containing the bin edges for the histogram. + """ + + # Convert to numpy to use histogram function + feature_correlation_arr = correlation_matrix.to_numpy() + + # Check if matrix is symmetric + if issymmetric(feature_correlation_arr): + print("Correlation matrix is symmetric.") + # Get only the bottom left triangle of the correlation matrix since the matrix is symmetric + lower_half_idx = np.mask_indices(feature_correlation_arr.shape[0], np.tril) + # This is a 1D array for binning and plotting + correlation_vals = feature_correlation_arr[lower_half_idx] + else: + # Flatten the matrix to a 1D array for binning and plotting + correlation_vals = feature_correlation_arr.flatten() + + # Set up figure and axes for the plot + dist_fig, dist_ax = plt.subplots() + + # Plot the histogram of correlation values + bin_values, bin_edges, _ = dist_ax.hist(correlation_vals, bins=num_bins) + + # Set up axis labels + dist_ax.set_xlabel(xlabel) + dist_ax.set_ylabel(ylabel) + + # Set axis bounds + dist_ax.set_xbound(-1.0, 1.0) + dist_ax.set_ybound(y_lower_bound, y_upper_bound) + + # Set title and subtitle + # Suptitle is the super title, which will be above the title + plt.suptitle(title, fontsize=14) + plt.title(subtitle, fontsize=10) + + return dist_fig, bin_values, bin_edges \ No newline at end of file From 0f9f3318629414fd9ed5a019573549eef0aeb175 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 12:02:58 -0500 Subject: [PATCH 10/40] feat: add correlation plot functions to init --- src/readii/analyze/__init__.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py index cfe1f83..b162ab7 100644 --- a/src/readii/analyze/__init__.py +++ b/src/readii/analyze/__init__.py @@ -1,10 +1,14 @@ """ Module to perform analysis on READII outputs """ from .correlation import getFeatureCorrelations, getVerticalSelfCorrelations, getHorizontalSelfCorrelations, getCrossCorrelationMatrix +from.plot_correlation import plotCorrelationHeatmap, plotCorrelationHistogram + __all__ = [ 'getFeatureCorrelations', 'getVerticalSelfCorrelations', 'getHorizontalSelfCorrelations', - 'getCrossCorrelationMatrix' + 'getCrossCorrelationMatrix', + 'plotCorrelationHeatmap', + 'plotCorrelationHistogram' ] \ No newline at end of file From 689eebfa1175a7b561006b34ccfaf10ecdc87eb1 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 14:30:22 -0500 Subject: [PATCH 11/40] feat: made writer class for plot figures --- src/readii/io/writers/plot_writer.py | 70 ++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 src/readii/io/writers/plot_writer.py diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py new file mode 100644 index 0000000..691fb3a --- /dev/null +++ b/src/readii/io/writers/plot_writer.py @@ -0,0 +1,70 @@ +from dataclasses import dataclass, field +from pathlib import Path + +import matplotlib.pyplot as plt + +from readii.io.writers.base_writer import BaseWriter +from readii.utils import logger + +class PlotWriterError(Exception): + """Base exception for PlotWriter errors.""" + + pass + + +class PlotWriterIOError(PlotWriterError): + """Raised when I/O operations fail.""" + + pass + +@dataclass +class PlotWriter(BaseWriter): + """Class for managing file writing with customizable paths and filenames for plot figure files.""" + + overwrite: bool = field( + default=False, + metadata={ + "help": "If True, allows overwriting existing files. If False, raises FileExistsError." + }, + ) + + def save(self, plot:plt.figure, **kwargs: str) -> Path: + """Save the plot to a .png file.""" + + logger.debug("Saving.", kwargs=kwargs) + + # Generate the output path + out_path = self.resolve_path(**kwargs) + + # Check if the output path already exists + if out_path.exists(): + if not self.overwrite: + msg = f"File {out_path} already exists. \nSet {self.__class__.__name__}.overwrite to True to overwrite." + raise PlotWriterIOError(msg) + else: + logger.warning(f"File {out_path} already exists. Overwriting.") + + logger.debug("Saving plot to file", out_path=out_path) + try: + # Save the plot to the output path, remove extra whitespace around the figure + plot.get_figure().savefig(out_path, bbox_inches='tight') + + except Exception as e: + msg = f"Error saving plot to file {out_path}: {e}" + raise PlotWriterIOError(msg) from e + else: + logger.info("Plot saved successfully.", out_path=out_path) + return out_path + + +if __name__ == "__main__": # pragma: no cover + from rich import print # noqa + + plot_writer = PlotWriter( + root_directory=Path("TRASH", "plot_writer_examples"), + filename_format="{DatasetName}_{PlotType}_{FeatureType}_{ImageType}_plot.png", + overwrite=True, + create_dirs=True + ) + + print(plot_writer) \ No newline at end of file From 23c87e405f65c7f38d21b9f009a0d7aa449801b7 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 14:32:40 -0500 Subject: [PATCH 12/40] fix: removing what I think is a typo import --- notebooks/nifti_writer_example.ipynb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/notebooks/nifti_writer_example.ipynb b/notebooks/nifti_writer_example.ipynb index 685c59a..20da7dd 100644 --- a/notebooks/nifti_writer_example.ipynb +++ b/notebooks/nifti_writer_example.ipynb @@ -16,7 +16,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -26,7 +26,6 @@ "import subprocess\n", "import SimpleITK as sitk\n", "import pandas as pd\n", - "import uuid\n", "import random\n", "import sys\n", "from readii.utils import logger" @@ -41,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -65,7 +64,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [ { @@ -210,7 +209,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.8" } }, "nbformat": 4, From de87bef50955298f9bcabba42a65dfa7c92d1e1f Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 14:37:10 -0500 Subject: [PATCH 13/40] style: add space in import statement for plot correlation --- src/readii/analyze/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py index b162ab7..7877fd0 100644 --- a/src/readii/analyze/__init__.py +++ b/src/readii/analyze/__init__.py @@ -1,7 +1,7 @@ """ Module to perform analysis on READII outputs """ from .correlation import getFeatureCorrelations, getVerticalSelfCorrelations, getHorizontalSelfCorrelations, getCrossCorrelationMatrix -from.plot_correlation import plotCorrelationHeatmap, plotCorrelationHistogram +from .plot_correlation import plotCorrelationHeatmap, plotCorrelationHistogram __all__ = [ From 6706b9fd18694ff790a39be412d7ca06e271626c Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 14:48:00 -0500 Subject: [PATCH 14/40] feat: add function return types --- src/readii/analyze/correlation.py | 8 ++++---- src/readii/analyze/plot_correlation.py | 6 ++++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 6381ce9..68808e3 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -5,7 +5,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, horizontal_features:pd.DataFrame, method:str = "pearson", vertical_feature_name:str = '_vertical', - horizontal_feature_name:str = '_horizontal'): + horizontal_feature_name:str = '_horizontal') -> pd.DataFrame: """ Function to calculate correlation between two sets of features. Parameters @@ -72,7 +72,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, - num_vertical_features:int): + num_vertical_features:int) -> pd.DataFrame: """ Function to get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. Parameters @@ -103,7 +103,7 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, - num_horizontal_features:int): + num_horizontal_features:int) -> pd.DataFrame: """ Function to get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. Parameters @@ -138,7 +138,7 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, - num_vertical_features:int): + num_vertical_features:int) -> pd.DataFrame: """ Function to get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. Parameters diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index 78cbc2a..b7bd97a 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -5,6 +5,8 @@ import pandas as pd from scipy.linalg import issymmetric +import matplotlib + from readii.utils import logger def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, @@ -16,7 +18,7 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, title:Optional[str] = "", subtitle:Optional[str] = "", show_tick_labels:bool = False - ): + ) -> matplotlib.figure.Figure: """Function to plot a correlation heatmap. Parameters @@ -102,7 +104,7 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, y_upper_bound:Optional[int] = None, title:Optional[str] = "Distribution of Correlations for Features", subtitle:Optional[str] = "", - ): + ) -> matplotlib.figure.Figure: """ Function to plot a distribution of correlation values for a correlation matrix. Parameters From 382de7305fd0bd2196d6e73dd18f1878f8ed2b72 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 14:48:26 -0500 Subject: [PATCH 15/40] feat: specify PlotWriter save object as matplotlib Figure --- src/readii/io/writers/plot_writer.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index 691fb3a..2b899aa 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -1,7 +1,7 @@ from dataclasses import dataclass, field from pathlib import Path -import matplotlib.pyplot as plt +import matplotlib from readii.io.writers.base_writer import BaseWriter from readii.utils import logger @@ -28,7 +28,7 @@ class PlotWriter(BaseWriter): }, ) - def save(self, plot:plt.figure, **kwargs: str) -> Path: + def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: """Save the plot to a .png file.""" logger.debug("Saving.", kwargs=kwargs) @@ -40,17 +40,19 @@ def save(self, plot:plt.figure, **kwargs: str) -> Path: if out_path.exists(): if not self.overwrite: msg = f"File {out_path} already exists. \nSet {self.__class__.__name__}.overwrite to True to overwrite." - raise PlotWriterIOError(msg) + logger.exception(msg) + raise FileExistsError(msg) else: logger.warning(f"File {out_path} already exists. Overwriting.") logger.debug("Saving plot to file", out_path=out_path) try: # Save the plot to the output path, remove extra whitespace around the figure - plot.get_figure().savefig(out_path, bbox_inches='tight') + plot.savefig(out_path, bbox_inches='tight') except Exception as e: msg = f"Error saving plot to file {out_path}: {e}" + logger.exception(msg) raise PlotWriterIOError(msg) from e else: logger.info("Plot saved successfully.", out_path=out_path) From b07e5a63206bd7dc2865e4385be96794ac779194 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 15:05:55 -0500 Subject: [PATCH 16/40] Merge remote-tracking branch 'origin/main' into katys/add-analysis --- .github/workflows/ci-cd.yml | 3 +- CHANGELOG.md | 24 + pixi.lock | 9276 ++++++++++++++++++++++++++++++----- pyproject.toml | 4 +- src/readii/__init__.py | 2 +- 5 files changed, 8039 insertions(+), 1270 deletions(-) diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index e9c5b0c..263dc50 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -16,7 +16,7 @@ jobs: timeout-minutes: 15 # Consider increasing timeout strategy: matrix: - os: [ubuntu-latest, macos-latest, macos-14] # , windows-latest removed for now + os: [ubuntu-latest, macos-latest, macos-14, windows-latest] # , windows-latest removed for now env: ["py310", "py311", "py312"] steps: @@ -28,7 +28,6 @@ jobs: environments: ${{ matrix.env }} pixi-version: v0.39.0 cache: true - locked: false # wont be the same because of the tag - name: Run pytest run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 8012dc9..6f6b43f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,30 @@ # CHANGELOG +## v1.26.0 (2024-12-16) + +### Features + +- Expand platform support in pixi and CI/CD workflow + ([#91](https://github.com/bhklab/readii/pull/91), + [`546fe5c`](https://github.com/bhklab/readii/commit/546fe5c1e4a4dff72645f2c61730d1acf0d13572)) + +This PR adds the windows platform and older mac platform to the pixi configuration so developers + with those machines can be assured that they can contribute to this project without running into + dependency issues + +- also add a testing branch to test with windows across all configured python versions + +## Summary by CodeRabbit + +- **New Features** - Expanded testing environment to include Windows support. - Updated project + version to "1.25.0". - Added support for additional platforms: "osx-64" and "win-64". + +- **Bug Fixes** - Clarified the checkout process for the publishing jobs in the CI-CD workflow. + + + + ## v1.25.0 (2024-12-16) ### Features diff --git a/pixi.lock b/pixi.lock index 4b6098b..9e8fe24 100644 --- a/pixi.lock +++ b/pixi.lock @@ -10,44 +10,29 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda - 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__osx >=11.0 - libzlib >=1.2.13,<2.0.0a0 + arch: arm64 + platform: osx license: BSD-3-Clause license_family: BSD purls: [] size: 405089 timestamp: 1714723101397 +- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.6-h0ea2cb4_0.conda + sha256: 768e30dc513568491818fb068ee867c57c514b553915536da09e5d10b4ebf3c3 + md5: 9a17230f95733c04dc40a2b1e5491d74 + depends: + - libzlib >=1.2.13,<2.0.0a0 + - ucrt >=10.0.20348.0 + - vc >=14.2,<15 + - vc14_runtime >=14.29.30139 + arch: x86_64 + platform: win + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 349143 + timestamp: 1714723445995 diff --git a/pyproject.toml b/pyproject.toml index 792e654..21e0154 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "readii" -version = "1.25.0" +version = "1.26.0" description = "A package to extract radiomic features!" authors = [{ name = "Katy Scott", email = "Katy.Scott@uhn.ca" }] @@ -34,7 +34,7 @@ readii-datasets = "readii.cli.main:cli" [tool.pixi.project] channels = ["conda-forge"] -platforms = ["linux-64", "osx-arm64"] +platforms = ["linux-64", "osx-arm64", "osx-64", "win-64"] [tool.pixi.dependencies] diff --git a/src/readii/__init__.py b/src/readii/__init__.py index 50bcc3a..69ad36a 100644 --- a/src/readii/__init__.py +++ b/src/readii/__init__.py @@ -1,4 +1,4 @@ # read version from installed package from importlib.metadata import version -__version__ = "1.25.0" +__version__ = "1.26.0" From 916c42b8843e10df834554de74a8bf800f962352 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:03:45 -0500 Subject: [PATCH 17/40] docs: correct docstring in getFeatureCorrelations for default feature name values Co-authored-by: Jermiah Joseph <44614774+jjjermiah@users.noreply.github.com> --- src/readii/analyze/correlation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 68808e3..f208251 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -17,9 +17,9 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, method : str Method to use for calculating correlations. Default is "pearson". vertical_feature_name : str - Name of the vertical features to use as suffix in correlation dataframe. Default is blank "". + Name of the vertical features to use as suffix in correlation dataframe. Default is "_vertical". horizontal_feature_name : str - Name of the horizontal features to use as suffix in correlation dataframe. Default is blank "". + Name of the horizontal features to use as suffix in correlation dataframe. Default is "_horizontal". Returns ------- From 24d41dd1ff4ac46a2b9dbc97d0498af4f5e7a902 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:06:00 -0500 Subject: [PATCH 18/40] docs: make function docstring oneliners imperative form --- src/readii/analyze/correlation.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index f208251..38263f5 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -6,7 +6,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, method:str = "pearson", vertical_feature_name:str = '_vertical', horizontal_feature_name:str = '_horizontal') -> pd.DataFrame: - """ Function to calculate correlation between two sets of features. + """ Calculate correlation between two sets of features. Parameters ---------- @@ -73,7 +73,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, num_vertical_features:int) -> pd.DataFrame: - """ Function to get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. + """ Get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. Parameters ---------- @@ -104,7 +104,7 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, num_horizontal_features:int) -> pd.DataFrame: - """ Function to get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. + """ Get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. Parameters ---------- @@ -139,7 +139,7 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, num_vertical_features:int) -> pd.DataFrame: - """ Function to get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. + """ Get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. Parameters ---------- From d917b7a99c7beabe12e17297d7a00c268c2cc53e Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:06:53 -0500 Subject: [PATCH 19/40] docs: make docstring oneliner imperative --- src/readii/analyze/plot_correlation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index b7bd97a..216334f 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -19,7 +19,7 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, subtitle:Optional[str] = "", show_tick_labels:bool = False ) -> matplotlib.figure.Figure: - """Function to plot a correlation heatmap. + """Plot a correlation dataframe as a heatmap. Parameters ---------- @@ -105,7 +105,7 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, title:Optional[str] = "Distribution of Correlations for Features", subtitle:Optional[str] = "", ) -> matplotlib.figure.Figure: - """ Function to plot a distribution of correlation values for a correlation matrix. + """Plot a histogram to show thedistribution of correlation values for a correlation matrix. Parameters ---------- From 293f40f3ea9cf24a56730f326f79244161496084 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:25:12 -0500 Subject: [PATCH 20/40] feat: add possible file extensions for plot figure, remove logger.exception calls --- src/readii/io/writers/plot_writer.py | 27 ++++++++++++++++++++++++--- 1 file changed, 24 insertions(+), 3 deletions(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index 2b899aa..7df4581 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -1,5 +1,6 @@ from dataclasses import dataclass, field from pathlib import Path +from typing import ClassVar import matplotlib @@ -17,6 +18,12 @@ class PlotWriterIOError(PlotWriterError): pass + +class PlotWriterValidationError(PlotWriterError): + """Raised when validation of writer configuration fails.""" + + pass + @dataclass class PlotWriter(BaseWriter): """Class for managing file writing with customizable paths and filenames for plot figure files.""" @@ -27,6 +34,22 @@ class PlotWriter(BaseWriter): "help": "If True, allows overwriting existing files. If False, raises FileExistsError." }, ) + # Make extensions immutable + VALID_EXTENSIONS: ClassVar[list[str]] = [ + ".png", + ".pdf", + ".ps", + ".eps", + ".svg" + ] + + def __post_init__(self) -> None: + """Validate writer configuration.""" + super().__post_init__() + + if not any(self.filename_format.endswith(ext) for ext in self.VALID_EXTENSIONS): + msg = f"Invalid filename format {self.filename_format}. Must end with one of {self.VALID_EXTENSIONS}." + raise PlotWriterValidationError(msg) def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: """Save the plot to a .png file.""" @@ -40,8 +63,7 @@ def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: if out_path.exists(): if not self.overwrite: msg = f"File {out_path} already exists. \nSet {self.__class__.__name__}.overwrite to True to overwrite." - logger.exception(msg) - raise FileExistsError(msg) + raise PlotWriterIOError(msg) else: logger.warning(f"File {out_path} already exists. Overwriting.") @@ -52,7 +74,6 @@ def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: except Exception as e: msg = f"Error saving plot to file {out_path}: {e}" - logger.exception(msg) raise PlotWriterIOError(msg) from e else: logger.info("Plot saved successfully.", out_path=out_path) From 7bd422ad80f7adc77cc6f6b8e4b290692a1b351b Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:25:50 -0500 Subject: [PATCH 21/40] refactor: replace print statement with logger --- src/readii/analyze/plot_correlation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index 216334f..84cb007 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -141,7 +141,7 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, # Check if matrix is symmetric if issymmetric(feature_correlation_arr): - print("Correlation matrix is symmetric.") + logger.debug("Correlation matrix is symmetric.") # Get only the bottom left triangle of the correlation matrix since the matrix is symmetric lower_half_idx = np.mask_indices(feature_correlation_arr.shape[0], np.tril) # This is a 1D array for binning and plotting From f564992f63635f462dbed90efeaba32115862bf1 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:26:25 -0500 Subject: [PATCH 22/40] docs: update triangle parameter description in plotCorrelationHeatmap --- src/readii/analyze/plot_correlation.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index 84cb007..3a82b26 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -28,7 +28,8 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, diagonal : bool, optional Whether to only plot half of the matrix. The default is False. triangle : str, optional - Which triangle half of the matrixto plot. The default is "lower". + Which triangle half of the matrix to plot. Either "lower" or "upper". + The default is "lower". xlabel : str, optional Label for the x-axis. The default is "". ylabel : str, optional From 9b1424a16e1fef17e821bbc2035ed6c228c32b25 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Mon, 16 Dec 2024 16:59:36 -0500 Subject: [PATCH 23/40] feat: add helper function to check if the subsetting of a dataframe is out of bounds for that dataframe --- src/readii/analyze/correlation.py | 41 +++++++++++---------------- src/readii/data/select.py | 47 ++++++++++++++++++++++++++++++- 2 files changed, 62 insertions(+), 26 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 38263f5..ea0fe0a 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -1,5 +1,6 @@ import pandas as pd from readii.utils import logger +from readii.data.select import validateDataframeSubsetSelection def getFeatureCorrelations(vertical_features:pd.DataFrame, horizontal_features:pd.DataFrame, @@ -87,15 +88,12 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, pd.DataFrame Dataframe containing the vertical self correlations from the correlation matrix. """ - if num_vertical_features > correlation_matrix.shape[0]: - msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." + try: + validateDataframeSubsetSelection(correlation_matrix, num_vertical_features, num_vertical_features) + except ValueError as e: + msg = f"Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) - raise ValueError() - - if num_vertical_features > correlation_matrix.shape[1]: - msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." - logger.exception(msg) - raise ValueError() + raise e # Get the correlation matrix for vertical vs vertical - this is the top left corner of the matrix return correlation_matrix.iloc[0:num_vertical_features, 0:num_vertical_features] @@ -118,16 +116,12 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, pd.DataFrame Dataframe containing the horizontal self correlations from the correlation matrix. """ - - if num_horizontal_features > correlation_matrix.shape[0]: - msg = f"Number of horizontal features ({num_horizontal_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." - logger.exception(msg) - raise ValueError() - - if num_horizontal_features > correlation_matrix.shape[1]: - msg = f"Number of horizontal features ({num_horizontal_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." + try: + validateDataframeSubsetSelection(correlation_matrix, num_horizontal_features, num_horizontal_features) + except ValueError as e: + msg = f"Number of horizontalfeatures provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) - raise ValueError() + raise e # Get the index of the start of the horizontal correlations start_of_horizontal_correlations = len(correlation_matrix.columns) - num_horizontal_features @@ -154,14 +148,11 @@ def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, Dataframe containing the cross correlations from the correlation matrix. """ - if num_vertical_features > correlation_matrix.shape[0]: - msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of rows in the correlation matrix ({correlation_matrix.shape[0]})." - logger.exception(msg) - raise ValueError() - - if num_vertical_features > correlation_matrix.shape[1]: - msg = f"Number of vertical features ({num_vertical_features}) is greater than the number of columns in the correlation matrix ({correlation_matrix.shape[1]})." + try: + validateDataframeSubsetSelection(correlation_matrix, num_vertical_features, num_vertical_features) + except ValueError as e: + msg = f"Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) - raise ValueError() + raise e return correlation_matrix.iloc[0:num_vertical_features, num_vertical_features:] \ No newline at end of file diff --git a/src/readii/data/select.py b/src/readii/data/select.py index f2d4a51..d854d40 100644 --- a/src/readii/data/select.py +++ b/src/readii/data/select.py @@ -174,4 +174,49 @@ def getPatientIntersectionDataframes(dataframe_A:DataFrame, intersection_index_dataframeA = dataframe_A.loc[intersection_index] intersection_index_dataframeB = dataframe_B.loc[intersection_index] - return intersection_index_dataframeA, intersection_index_dataframeB \ No newline at end of file + return intersection_index_dataframeA, intersection_index_dataframeB + + +def validateDataframeSubsetSelection(dataframe:DataFrame, + num_rows:Optional[int] = None, + num_cols:Optional[int] = None): + + # Check if dataframe is a DataFrame + if not isinstance(dataframe, DataFrame): + msg = f"dataframe must be a pandas DataFrame, got {type(dataframe)}" + logger.error(msg) + raise TypeError(msg) + + if num_rows is not None: + # Check if num_rows is an integer + if not isinstance(num_rows, int): + msg = f"num_rows must be an integer, got {type(num_rows)}" + logger.error(msg) + raise TypeError(msg) + + if num_rows > dataframe.shape[0]: + msg = f"num_rows ({num_rows}) is greater than the number of rows in the dataframe ({dataframe.shape[0]})" + logger.error(msg) + raise ValueError() + else: + logger.debug("Number of rows is within the size of the dataframe.") + + + if num_cols is not None: + # Check if num_cols is an integer + if not isinstance(num_cols, int): + msg = f"num_cols must be an integer, got {type(num_cols)}" + logger.error(msg) + raise TypeError(msg) + + if num_cols > dataframe.shape[1]: + msg = f"num_cols ({num_cols}) is greater than the number of columns in the dataframe ({dataframe.shape[1]})" + logger.error(msg) + raise ValueError() + else: + logger.debug("Number of columns is within the size of the dataframe.") + + return None + + + From 9af12897c01f6821fd11a63d1fe4d3a19985398f Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:19:22 -0500 Subject: [PATCH 24/40] docs/refactor: add parameter descriptions for PlotWriter save, change VALID_EXTENSIONS to a tuple --- src/readii/io/writers/plot_writer.py | 26 +++++++++++++++++++++++--- 1 file changed, 23 insertions(+), 3 deletions(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index 7df4581..e5d292d 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -35,13 +35,13 @@ class PlotWriter(BaseWriter): }, ) # Make extensions immutable - VALID_EXTENSIONS: ClassVar[list[str]] = [ + VALID_EXTENSIONS: ClassVar[list[str]] = ( ".png", ".pdf", ".ps", ".eps", ".svg" - ] + ) def __post_init__(self) -> None: """Validate writer configuration.""" @@ -52,7 +52,27 @@ def __post_init__(self) -> None: raise PlotWriterValidationError(msg) def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: - """Save the plot to a .png file.""" + """Save the plot to a .png file with extra whitespace removed. + + Parameters + ---------- + plot : matplotlib.figure.Figure + The plot to save. + kwargs : dict + Additional keyword arguments to pass to the save method. + + Returns + ------- + Path + The path to the saved file. + + Raises + ------ + PlotWriterIOError + If there is an error saving the plot. + PlotWriterValidationError + If the filename format is invalid. + """ logger.debug("Saving.", kwargs=kwargs) From 5406928cae8828842e71b798a69eeed30b8f0c60 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:22:11 -0500 Subject: [PATCH 25/40] style: remove blank line after function docstring --- src/readii/io/writers/plot_writer.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index e5d292d..b9647fa 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -73,7 +73,6 @@ def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: PlotWriterValidationError If the filename format is invalid. """ - logger.debug("Saving.", kwargs=kwargs) # Generate the output path From 573f8a970a07ba9e36abc14023e893789c1a8629 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:23:55 -0500 Subject: [PATCH 26/40] refactor: remove unused import --- src/readii/image_processing.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/readii/image_processing.py b/src/readii/image_processing.py index 94379fa..a64dc4e 100644 --- a/src/readii/image_processing.py +++ b/src/readii/image_processing.py @@ -8,7 +8,6 @@ from readii.loaders import ( loadDicomSITK, - loadRTSTRUCTSITK, loadSegmentation, ) From d3f713e0b325b196533a7caef429715999cbe006 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:24:46 -0500 Subject: [PATCH 27/40] refactor: remove unused error variables in loadFeatureFilesFromImageTypes --- src/readii/io/loaders/features.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py index a499798..b7dbbde 100644 --- a/src/readii/io/loaders/features.py +++ b/src/readii/io/loaders/features.py @@ -53,7 +53,7 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, image_type_feature_file = matching_files[0] # Remove the image type file from the list of feature files feature_file_list.remove(image_type_feature_file) - except IndexError as e: + except IndexError: logger.warning(f"No {image_type} feature csv files found in {extracted_feature_dir}") # Skip to the next image type continue @@ -70,7 +70,7 @@ def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, if drop_labels: # Data is now only extracted features raw_feature_data.drop(labels_to_drop, axis=1, inplace=True) - except KeyError as e: + except KeyError: logger.warning(f"{feature_file_path} does not have the labels {labels_to_drop} to drop.") # Skip to the next image type continue From 0012f6ea6819e5c0af22b192189e8da2e66d4a68 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:25:17 -0500 Subject: [PATCH 28/40] refactor: change fstring to regular string in error msgs --- src/readii/analyze/correlation.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index ea0fe0a..0909051 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -91,7 +91,7 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, try: validateDataframeSubsetSelection(correlation_matrix, num_vertical_features, num_vertical_features) except ValueError as e: - msg = f"Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." + msg = "Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) raise e @@ -119,7 +119,7 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, try: validateDataframeSubsetSelection(correlation_matrix, num_horizontal_features, num_horizontal_features) except ValueError as e: - msg = f"Number of horizontalfeatures provided is greater than the number of rows or columns in the correlation matrix." + msg = "Number of horizontalfeatures provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) raise e @@ -151,7 +151,7 @@ def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, try: validateDataframeSubsetSelection(correlation_matrix, num_vertical_features, num_vertical_features) except ValueError as e: - msg = f"Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." + msg = "Number of vertical features provided is greater than the number of rows or columns in the correlation matrix." logger.exception(msg) raise e From 16c989bdf1e3f715fa1a538a175d79d1e212e610 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:35:25 -0500 Subject: [PATCH 29/40] style: remove whitespace around docstrings --- src/readii/analyze/__init__.py | 4 +--- src/readii/analyze/correlation.py | 1 - src/readii/analyze/plot_correlation.py | 2 -- 3 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py index 7877fd0..90d5f56 100644 --- a/src/readii/analyze/__init__.py +++ b/src/readii/analyze/__init__.py @@ -1,9 +1,7 @@ -""" Module to perform analysis on READII outputs """ - +"""Module to perform analysis on READII outputs.""" from .correlation import getFeatureCorrelations, getVerticalSelfCorrelations, getHorizontalSelfCorrelations, getCrossCorrelationMatrix from .plot_correlation import plotCorrelationHeatmap, plotCorrelationHistogram - __all__ = [ 'getFeatureCorrelations', 'getVerticalSelfCorrelations', diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 0909051..17b93a6 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -147,7 +147,6 @@ def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, pd.DataFrame Dataframe containing the cross correlations from the correlation matrix. """ - try: validateDataframeSubsetSelection(correlation_matrix, num_vertical_features, num_vertical_features) except ValueError as e: diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index 3a82b26..c6ca152 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -46,7 +46,6 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, corr_fig : matplotlib.pyplot.figure Figure object containing a Seaborn heatmap. """ - if diagonal: logger.debug(f"Creating {triangle} traingle mask for diagonal correlation plot.") # Set up mask for hiding half the matrix in the plot @@ -136,7 +135,6 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, bin_edges : np.ndarray Numpy array containing the bin edges for the histogram. """ - # Convert to numpy to use histogram function feature_correlation_arr = correlation_matrix.to_numpy() From 657b72a81645792d2c33deb9a6f178f851c8ceea Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:35:45 -0500 Subject: [PATCH 30/40] feat: add all io, data, analyze functions to ruff config --- config/ruff.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/config/ruff.toml b/config/ruff.toml index 935bf10..0ddb2e1 100644 --- a/config/ruff.toml +++ b/config/ruff.toml @@ -6,7 +6,9 @@ include = [ "src/readii/feature_extraction.py", "src/readii/cli/**/*.py", "src/readii/negative_controls_refactor/**.py", - "src/readii/io/writers/**.py", + "src/readii/io/**/**.py", + "src/readii/data/**.py", + "src/readii/analyze/**.py" ] # extend-exclude is used to exclude directories from the flake8 checks From 6dee1267aac1f0bffa901ba072cfad44650bbcf7 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:37:39 -0500 Subject: [PATCH 31/40] style: sorted imports --- src/readii/analyze/plot_correlation.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index c6ca152..c5bccfb 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -1,14 +1,15 @@ from typing import Optional + +import matplotlib import matplotlib.pyplot as plt -import seaborn as sns import numpy as np import pandas as pd +import seaborn as sns from scipy.linalg import issymmetric -import matplotlib - from readii.utils import logger + def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, diagonal:bool = False, triangle:Optional[str] = "lower", From cd12dd26102395ec395456b035d81ffeeaad7227 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:39:25 -0500 Subject: [PATCH 32/40] refactor: replaced matplotlib import to specifically import Figure --- src/readii/analyze/plot_correlation.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index c5bccfb..3b7ed2b 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -1,10 +1,10 @@ from typing import Optional -import matplotlib import matplotlib.pyplot as plt import numpy as np import pandas as pd import seaborn as sns +from matplotlib.figure import Figure from scipy.linalg import issymmetric from readii.utils import logger @@ -19,7 +19,7 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, title:Optional[str] = "", subtitle:Optional[str] = "", show_tick_labels:bool = False - ) -> matplotlib.figure.Figure: + ) -> Figure: """Plot a correlation dataframe as a heatmap. Parameters @@ -105,7 +105,7 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, y_upper_bound:Optional[int] = None, title:Optional[str] = "Distribution of Correlations for Features", subtitle:Optional[str] = "", - ) -> matplotlib.figure.Figure: + ) -> Figure: """Plot a histogram to show thedistribution of correlation values for a correlation matrix. Parameters From ce56c78d9ce9ae41b4ee615ba4142726e5bba63a Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:40:48 -0500 Subject: [PATCH 33/40] style: sort imports, remove whitespace in docstring --- src/readii/analyze/correlation.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 17b93a6..0515bb8 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -1,13 +1,15 @@ import pandas as pd -from readii.utils import logger + from readii.data.select import validateDataframeSubsetSelection +from readii.utils import logger + def getFeatureCorrelations(vertical_features:pd.DataFrame, horizontal_features:pd.DataFrame, method:str = "pearson", vertical_feature_name:str = '_vertical', horizontal_feature_name:str = '_horizontal') -> pd.DataFrame: - """ Calculate correlation between two sets of features. + """Calculate correlation between two sets of features. Parameters ---------- @@ -74,7 +76,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, num_vertical_features:int) -> pd.DataFrame: - """ Get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. + """Get the vertical (y-axis) self correlations from a correlation matrix. Gets the top left quadrant of the correlation matrix. Parameters ---------- @@ -102,7 +104,7 @@ def getVerticalSelfCorrelations(correlation_matrix:pd.DataFrame, def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, num_horizontal_features:int) -> pd.DataFrame: - """ Get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. + """Get the horizontal (x-axis) self correlations from a correlation matrix. Gets the bottom right quadrant of the correlation matrix. Parameters ---------- @@ -133,7 +135,7 @@ def getHorizontalSelfCorrelations(correlation_matrix:pd.DataFrame, def getCrossCorrelationMatrix(correlation_matrix:pd.DataFrame, num_vertical_features:int) -> pd.DataFrame: - """ Get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. + """Get the cross correlation matrix subsection for a correlation matrix. Gets the top right quadrant of the correlation matrix so vertical and horizontal features are correctly labeled. Parameters ---------- From b62b735619ed74bb260dfa8d4dbe3a9e45fda7a7 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 09:41:23 -0500 Subject: [PATCH 34/40] style: sort imports --- src/readii/analyze/__init__.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py index 90d5f56..73b5a90 100644 --- a/src/readii/analyze/__init__.py +++ b/src/readii/analyze/__init__.py @@ -1,5 +1,10 @@ """Module to perform analysis on READII outputs.""" -from .correlation import getFeatureCorrelations, getVerticalSelfCorrelations, getHorizontalSelfCorrelations, getCrossCorrelationMatrix +from .correlation import ( + getCrossCorrelationMatrix, + getFeatureCorrelations, + getHorizontalSelfCorrelations, + getVerticalSelfCorrelations, +) from .plot_correlation import plotCorrelationHeatmap, plotCorrelationHistogram __all__ = [ From 64052c0ba461b026d6673e046d393138402a04b3 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 10:02:39 -0500 Subject: [PATCH 35/40] feat: add error handling --- src/readii/analyze/plot_correlation.py | 28 ++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/src/readii/analyze/plot_correlation.py b/src/readii/analyze/plot_correlation.py index 3b7ed2b..8ebf068 100644 --- a/src/readii/analyze/plot_correlation.py +++ b/src/readii/analyze/plot_correlation.py @@ -73,11 +73,16 @@ def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, corr_fig, corr_ax = plt.subplots() # Plot the correlation matrix - corr_ax = sns.heatmap(correlation_matrix_df, - mask = mask, - cmap=cmap, - vmin=-1.0, - vmax=1.0) + try: + corr_ax = sns.heatmap(correlation_matrix_df, + mask = mask, + cmap=cmap, + vmin=-1.0, + vmax=1.0) + except Exception as e: + msg = f"Error generating heatmap: {e}" + logger.exception(msg) + raise e if not show_tick_labels: # Remove the individual feature names from the axes @@ -154,7 +159,18 @@ def plotCorrelationHistogram(correlation_matrix:pd.DataFrame, dist_fig, dist_ax = plt.subplots() # Plot the histogram of correlation values - bin_values, bin_edges, _ = dist_ax.hist(correlation_vals, bins=num_bins) + # Validate num_bins + if num_bins <= 0: + msg = f"Number of bins must be positive, got {num_bins}" + logger.exception(msg) + raise ValueError() + + try: + bin_values, bin_edges, _ = dist_ax.hist(correlation_vals, bins=num_bins) + except Exception as e: + msg = f"Error generating histogram: {e}" + logger.exception(msg) + raise e # Set up axis labels dist_ax.set_xlabel(xlabel) From 4cf18a4d2afd11d0ab161a83e69b971302d2296c Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 10:03:00 -0500 Subject: [PATCH 36/40] refactor: correct help message for overwrite --- src/readii/io/writers/plot_writer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index b9647fa..4f17d4f 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -31,7 +31,7 @@ class PlotWriter(BaseWriter): overwrite: bool = field( default=False, metadata={ - "help": "If True, allows overwriting existing files. If False, raises FileExistsError." + "help": "If True, allows overwriting existing files. If False, raises PlotWriterIOError." }, ) # Make extensions immutable From 227e02a643ef8a5a2322ecb900aeb60c4b10627e Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 11:39:43 -0500 Subject: [PATCH 37/40] refactor: replace matplotlib import with Figure import --- src/readii/io/writers/plot_writer.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index 4f17d4f..7f01b57 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -1,9 +1,8 @@ from dataclasses import dataclass, field from pathlib import Path +from matplotlib.figure import Figure from typing import ClassVar -import matplotlib - from readii.io.writers.base_writer import BaseWriter from readii.utils import logger @@ -51,7 +50,7 @@ def __post_init__(self) -> None: msg = f"Invalid filename format {self.filename_format}. Must end with one of {self.VALID_EXTENSIONS}." raise PlotWriterValidationError(msg) - def save(self, plot:matplotlib.figure.Figure, **kwargs: str) -> Path: + def save(self, plot:Figure, **kwargs: str) -> Path: """Save the plot to a .png file with extra whitespace removed. Parameters From d583a8413b4891845345aac9bbc865b8933681a2 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 11:40:18 -0500 Subject: [PATCH 38/40] style: sort imports --- src/readii/io/writers/plot_writer.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/readii/io/writers/plot_writer.py b/src/readii/io/writers/plot_writer.py index 7f01b57..3effc80 100644 --- a/src/readii/io/writers/plot_writer.py +++ b/src/readii/io/writers/plot_writer.py @@ -1,11 +1,13 @@ from dataclasses import dataclass, field from pathlib import Path -from matplotlib.figure import Figure from typing import ClassVar +from matplotlib.figure import Figure + from readii.io.writers.base_writer import BaseWriter from readii.utils import logger + class PlotWriterError(Exception): """Base exception for PlotWriter errors.""" From 173b2127acda91340bb47fd66404efbdb703374f Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 11:40:55 -0500 Subject: [PATCH 39/40] refactor: remove io readers and data directory for now, will add in separate branch --- config/ruff.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config/ruff.toml b/config/ruff.toml index 0ddb2e1..f1f5a6c 100644 --- a/config/ruff.toml +++ b/config/ruff.toml @@ -6,8 +6,7 @@ include = [ "src/readii/feature_extraction.py", "src/readii/cli/**/*.py", "src/readii/negative_controls_refactor/**.py", - "src/readii/io/**/**.py", - "src/readii/data/**.py", + "src/readii/io/writers/**.py", "src/readii/analyze/**.py" ] From 5be183138a153394a74db0b0d11babc8ce5fb10e Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 17 Dec 2024 11:42:11 -0500 Subject: [PATCH 40/40] feat: add check for empty dataframes in getFeatureCorrelations --- src/readii/analyze/correlation.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 0515bb8..6de9a93 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -38,6 +38,12 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, msg = "horizontal_features must be a pandas DataFrame" logger.exception(msg) raise TypeError() + + # Check for empty DataFrames + if vertical_features.empty or horizontal_features.empty: + msg = "Cannot calculate correlations with empty DataFrames" + logger.exception(msg) + raise ValueError(msg) if method not in ["pearson", "spearman", "kendall"]: msg = "Correlation method must be one of 'pearson', 'spearman', or 'kendall'."