From 95586e5eca119e5246c4dab800f64dab11d704bf Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:08:53 -0500 Subject: [PATCH 01/16] feat: add function to calculate feature correlation matrix --- src/readii/analyze/correlation.py | 44 +++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 src/readii/analyze/correlation.py diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py new file mode 100644 index 0000000..90d7a05 --- /dev/null +++ b/src/readii/analyze/correlation.py @@ -0,0 +1,44 @@ +import pandas as pd +from typing import Optional +import matplotlib.pyplot as plt +import seaborn as sns +import numpy as np +from scipy.linalg import issymmetric + + +def getFeatureCorrelations(vertical_features:pd.DataFrame, + horizontal_features:pd.DataFrame, + method:Optional[str] = "pearson", + vertical_feature_name:Optional[str] = "", + horizontal_feature_name:Optional[str] = ""): + """ Function to calculate correlation between two sets of features. + + Parameters + ---------- + vertical_features : pd.DataFrame + Dataframe containing features to calculate correlations with. + horizontal_features : pd.DataFrame + Dataframe containing features to calculate correlations with. + 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. + """ + # 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=f"_{vertical_feature_name}", + rsuffix=f"_{horizontal_feature_name}") + + # Calculate correlation between vertical features and horizontal features + correlation_matrix = features_to_correlate.corr(method=method) + + return correlation_matrix From 5193fb44c50b462a41d69f38273154c9a6f21543 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:09:35 -0500 Subject: [PATCH 02/16] feat: add function to generate a heatmap plot figure from a correlation matrix --- src/readii/analyze/correlation.py | 82 +++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 90d7a05..09175ba 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -42,3 +42,85 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, correlation_matrix = features_to_correlate.corr(method=method) return correlation_matrix + + +def plotCorrelationHeatmap(correlation_matrix_df:pd.DataFrame, + diagonal:Optional[bool] = False, + triangle:Optional[str] = "lower", + cmap:Optional[str] = "nipy_spectral", + xlabel:Optional[str] = "", + ylabel:Optional[str] = "", + title:Optional[str] = "", + subtitle:Optional[str] = "", + show_tick_labels:Optional[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: + # 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: + raise ValueError("If diagonal is True, triangle must be either 'lower' or 'upper'.") + else: + # 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 From a0771c6fdef52285cd050f5fb8328afdb76cb670 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:10:35 -0500 Subject: [PATCH 03/16] feat: add init file to analyze directory --- src/readii/analyze/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 src/readii/analyze/__init__.py diff --git a/src/readii/analyze/__init__.py b/src/readii/analyze/__init__.py new file mode 100644 index 0000000..e69de29 From cf26afca4afdce922833c56800c41ffe759bb7f8 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:23:33 -0500 Subject: [PATCH 04/16] feat: add error handling in getFeatureCorrelations --- src/readii/analyze/correlation.py | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 09175ba..3e00bdb 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -16,9 +16,9 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, Parameters ---------- vertical_features : pd.DataFrame - Dataframe containing features to calculate correlations with. + 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. + 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 @@ -31,15 +31,24 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, correlation_matrix : pd.DataFrame Dataframe containing correlation values. """ + if method not in ["pearon", "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.") + # 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=f"_{vertical_feature_name}", - rsuffix=f"_{horizontal_feature_name}") + how='inner', + lsuffix=f"_{vertical_feature_name}", + rsuffix=f"_{horizontal_feature_name}") - # Calculate correlation between vertical features and horizontal features - correlation_matrix = features_to_correlate.corr(method=method) + 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 From e64334925db133426ef1034d7fb10d947d36df63 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:38:10 -0500 Subject: [PATCH 05/16] feat: add general loading file, add loading config and data file functions --- src/readii/io/loaders/general.py | 76 ++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 src/readii/io/loaders/general.py diff --git a/src/readii/io/loaders/general.py b/src/readii/io/loaders/general.py new file mode 100644 index 0000000..c7bc157 --- /dev/null +++ b/src/readii/io/loaders/general.py @@ -0,0 +1,76 @@ +import itertools +import numpy as np +import os +import pandas as pd +import re +import yaml + +from pandas import DataFrame +from seaborn import heatmap + +from typing import Optional, Dict, Union + + +def loadImageDatasetConfig(dataset_name:str, + config_dir_path:str) -> dict: + """Load the configuration file for a given dataset. Expects the configuration file to be named .yaml. + + Parameters + ---------- + dataset_name : str + Name of the dataset to load the configuration file for. + config_dir_path : str + Path to the directory containing the configuration files. + + Returns + ------- + dict + Dictionary containing the configuration settings for the dataset. + + Examples + -------- + >>> config = loadImageDatasetConfig("NSCLC_Radiogenomics", "config/") + """ + # Make full path to config file + config_file_path = os.path.join(config_dir_path, f"{dataset_name}.yaml") + + # Check if config file exists + if os.path.exists(config_file_path): + # Load the config file + config = yaml.safe_load(open(config_file_path, "r")) + return config + else: + print(f"Config file {config_file_path} does not exist.") + return None + + + +def loadFileToDataFrame(file_path:str) -> pd.DataFrame: + """Load data from a csv or xlsx file into a pandas dataframe. + + Parameters + ---------- + file_path (str): Path to the data file. + + Returns + ------- + pd.DataFrame: Dataframe containing the data from the file. + """ + # Get the file extension + _, file_extension = os.path.splitext(file_path) + + try: + # Check if the file is an Excel file + if file_extension == '.xlsx': + df = pd.read_excel(file_path) + # Check if the file is a CSV file + elif file_extension == '.csv': + df = pd.read_csv(file_path) + else: + raise ValueError("Unsupported file format. Please provide a .csv or .xlsx file.") + + return df + + except Exception as e: + print(f"An error occurred: {e}") + return None \ No newline at end of file From f5882da996f67f62790f7881749e1e7315c1eeca Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 11:53:21 -0500 Subject: [PATCH 06/16] feat: add file for loading functions related to feature files --- src/readii/io/loaders/features.py | 70 +++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 src/readii/io/loaders/features.py diff --git a/src/readii/io/loaders/features.py b/src/readii/io/loaders/features.py new file mode 100644 index 0000000..a38c024 --- /dev/null +++ b/src/readii/io/loaders/features.py @@ -0,0 +1,70 @@ +import os +import pandas as pd + +from typing import Optional, Dict + +from readii.io.loaders.general import loadFileToDataFrame + + +def loadFeatureFilesFromImageTypes(extracted_feature_dir:str, + image_types:Optional[list]=['original'], + drop_labels:Optional[bool]=True, + labels_to_drop:Optional[list]=["patient_ID","survival_time_in_years","survival_event_binary"])->Dict[str,pd.DataFrame]: + """Function to load in all the extracted imaging feature sets from a directory and return them as a dictionary of dataframes. + + Parameters + ---------- + extracted_feature_dir : str + Path to the directory containing the extracted feature csv files + image_types : list, optional + List of image types to load in. The default is ['original']. + drop_labels : bool, optional + Whether to drop the labels from the dataframes. Use when loading labelled data from data_setup_for_modeling.ipynb. The default is True. + labels_to_drop : list, optional + List of labels to drop from the dataframes. The default is ["patient_ID","survival_time_in_years","survival_event_binary"] based on code + in data_setup_for_modeling.ipynb. + + Returns + ------- + feature_sets : dict + Dictionary of dataframes containing the extracted radiomics features. + """ + # Initialize dictionary to store the feature sets + feature_sets = {} + + feature_file_list = os.listdir(extracted_feature_dir) + + # Loop through all the files in the directory + for image_type in image_types: + try: + # Extract the image type feature csv file from the feature directory + # This should return a list of length 1, so we can just take the first element + image_type_feature_file = [file for file in feature_file_list if (image_type in file) and (file.endswith(".csv"))][0] + # Remove the image type file from the list of feature files + feature_file_list.remove(image_type_feature_file) + except Exception as e: + print(f"{e}\n No {image_type} feature csv files found in {extracted_feature_dir}") + # Skip to the next image type + continue + + + # Get the full path to the feature file + feature_file_path = os.path.join(extracted_feature_dir, image_type_feature_file) + + # Load the feature data into a pandas dataframe + raw_feature_data = loadFileToDataFrame(feature_file_path) + + try: + # Drop the labels from the dataframe if specified + if drop_labels: + # Data is now only extracted features + raw_feature_data.drop(labels_to_drop, axis=1, inplace=True) + except Exception as e: + print(f"{feature_file_path} does not have the labels {labels_to_drop} to drop.") + # Skip to the next image type + continue + + # Save the dataframe to the feature_sets dictionary + feature_sets[image_type] = raw_feature_data + + return feature_sets \ No newline at end of file From 5495550ca605b31deb7a183f25c3e6c0e2b14fd5 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 16:59:26 -0500 Subject: [PATCH 07/16] build: add numpy and seaborn for correlation code --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 4d14cc2..1f29b42 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -189,3 +189,5 @@ publish-test = { cmd = [ jupyterlab = ">=4.3.1,<5" pixi-kernel = ">=0.5.1,<0.6" ipykernel = ">=6.29.5,<7" +numpy = "1.26.4.*" +seaborn = ">=0.13.2,<0.14" From decf8e57f4daaf10f4b5f0f346235ba5c69f4f5e Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 16:59:41 -0500 Subject: [PATCH 08/16] refactor: remove so far unused imports --- src/readii/io/loaders/general.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/readii/io/loaders/general.py b/src/readii/io/loaders/general.py index c7bc157..87fdfaa 100644 --- a/src/readii/io/loaders/general.py +++ b/src/readii/io/loaders/general.py @@ -1,13 +1,7 @@ -import itertools -import numpy as np import os import pandas as pd -import re import yaml -from pandas import DataFrame -from seaborn import heatmap - from typing import Optional, Dict, Union From fcc1b9e4d475934ef54fec74052d6ed61db2cb56 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 16:59:57 -0500 Subject: [PATCH 09/16] feat: started test function for getFeatureCorrelations --- tests/test_correlation.py | 44 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 tests/test_correlation.py diff --git a/tests/test_correlation.py b/tests/test_correlation.py new file mode 100644 index 0000000..29ef275 --- /dev/null +++ b/tests/test_correlation.py @@ -0,0 +1,44 @@ +from readii.analyze.correlation import ( + getFeatureCorrelations, + plotCorrelationHeatmap, +) + +import pytest +import collections +import pandas as pd +import os + +@pytest.fixture +def nsclc_radiomic_features(): + return pd.read_csv("tests/output/features/radiomicfeatures_original_NSCLC_Radiogenomics.csv") + +@pytest.fixture +def lung4D_radiomic_features(): + return pd.read_csv("tests/output/features/radiomicfeatures_original_4D-Lung.csv") + + +@pytest.mark.parametrize( + "features", + [ + ("nsclc_radiomic_features"), + ("lung4D_radiomic_features") + ], + "correlation_method", + [ + ("pearson"), + ("spearman"), + ("random") + ] +) +def test_getFeatureCorrelations(features, correlation_method, request): + """Test getting correlation matrix for a set of features""" + features = request.getfixturevalue(features) + correlation_method = request.getfixturevalue(correlation_method) + actual = getFeatureCorrelations(vertical_features = features, + horizontal_features = features, + method = correlation_method + ) + assert isinstance(actual, pd.DataFrame), \ + "Wrong return type, expect a pandas DataFrame" + assert actual.shape[0] == 2*features.shape[1], \ + "Wrong return size, should be the same as the number of features" \ No newline at end of file From a7081826a778a7b058e2569c7fa5a877acbcf1ff Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Tue, 3 Dec 2024 17:00:23 -0500 Subject: [PATCH 10/16] feat: make files for better function organization --- src/readii/data/labelling.py | 0 src/readii/io/loaders/images.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 src/readii/data/labelling.py create mode 100644 src/readii/io/loaders/images.py diff --git a/src/readii/data/labelling.py b/src/readii/data/labelling.py new file mode 100644 index 0000000..e69de29 diff --git a/src/readii/io/loaders/images.py b/src/readii/io/loaders/images.py new file mode 100644 index 0000000..e69de29 From d63a1c548c5059f224426551811729aa0de0e2f8 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 15:38:40 -0500 Subject: [PATCH 11/16] fix: remove duplicate tool.pixi.dependencies from merge --- pyproject.toml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 754c0e5..7f2d64d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -192,9 +192,3 @@ publish-test = { cmd = [ "build", ], description = "Publish to test PyPI" } -[tool.pixi.dependencies] -jupyterlab = ">=4.3.1,<5" -pixi-kernel = ">=0.5.1,<0.6" -ipykernel = ">=6.29.5,<7" -numpy = "1.26.4.*" -seaborn = ">=0.13.2,<0.14" From 484c12e35ea2e8d37d05c556c6a3e7b4e37a4bae Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 16:14:23 -0500 Subject: [PATCH 12/16] build: add seaborn for correlation plot functions, need to specify numpy for seaborn install to work --- pixi.lock | 9718 ++++++++++++++++++++++++++++++++---------------- pyproject.toml | 2 + 2 files changed, 6546 insertions(+), 3174 deletions(-) diff --git a/pixi.lock b/pixi.lock index 271a3b7..3011739 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,4 +1,4 @@ -version: 6 +version: 5 environments: default: channels: @@ -9,131 +9,208 @@ environments: linux-64: - 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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: [] diff --git a/pyproject.toml b/pyproject.toml index 7f2d64d..5502cce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,8 @@ channels = ["conda-forge"] platforms = ["linux-64", "osx-arm64"] [tool.pixi.dependencies] +numpy = "1.26.4.*" +seaborn = ">=0.13.2,<0.14" [tool.pixi.pypi-dependencies] From c6b945fe90950e71d3213a2f426ccb5a6a9204b1 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 16:17:32 -0500 Subject: [PATCH 13/16] feat: add init files for new directories --- src/readii/__init__.py | 1 - src/readii/io/__init__.py | 0 src/readii/io/loaders/__init__.py | 0 src/readii/io/writers/__init__.py | 0 4 files changed, 1 deletion(-) create mode 100644 src/readii/io/__init__.py create mode 100644 src/readii/io/loaders/__init__.py create mode 100644 src/readii/io/writers/__init__.py diff --git a/src/readii/__init__.py b/src/readii/__init__.py index a48da87..72452f7 100644 --- a/src/readii/__init__.py +++ b/src/readii/__init__.py @@ -1,4 +1,3 @@ # read version from installed package from importlib.metadata import version __version__ = "1.18.0" - diff --git a/src/readii/io/__init__.py b/src/readii/io/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/readii/io/loaders/__init__.py b/src/readii/io/loaders/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/readii/io/writers/__init__.py b/src/readii/io/writers/__init__.py new file mode 100644 index 0000000..e69de29 From fc83d69cef19cc55a05c294c0cb8b85025968f49 Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 16:18:19 -0500 Subject: [PATCH 14/16] feat: add function to calculate feature correlations and a function to plot them as a heatmap --- src/readii/analyze/correlation.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/readii/analyze/correlation.py b/src/readii/analyze/correlation.py index 3e00bdb..959a55c 100644 --- a/src/readii/analyze/correlation.py +++ b/src/readii/analyze/correlation.py @@ -8,7 +8,7 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, horizontal_features:pd.DataFrame, - method:Optional[str] = "pearson", + method:str = "pearson", vertical_feature_name:Optional[str] = "", horizontal_feature_name:Optional[str] = ""): """ Function to calculate correlation between two sets of features. @@ -31,18 +31,26 @@ def getFeatureCorrelations(vertical_features:pd.DataFrame, correlation_matrix : pd.DataFrame Dataframe containing correlation values. """ - if method not in ["pearon", "spearman", "kendall"]: + # Check that features are dataframes + assert isinstance(vertical_features, pd.DataFrame), "vertical_features must be a pandas DataFrame" + assert isinstance(horizontal_features, pd.DataFrame), "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 are not blank so they can be used as suffixes + if vertical_feature_name: vertical_feature_name = f"_{vertical_feature_name}" + if horizontal_feature_name: 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=f"_{vertical_feature_name}", - rsuffix=f"_{horizontal_feature_name}") + lsuffix=vertical_feature_name, + rsuffix=horizontal_feature_name) try: # Calculate correlation between vertical features and horizontal features From 46f077368f986c8bd06ccda44226f8401b581c3c Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 16:18:47 -0500 Subject: [PATCH 15/16] feat: add function to drop a set of features at the beginning of a pands dataframe based on a column name --- src/readii/data/process.py | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 src/readii/data/process.py diff --git a/src/readii/data/process.py b/src/readii/data/process.py new file mode 100644 index 0000000..489195c --- /dev/null +++ b/src/readii/data/process.py @@ -0,0 +1,43 @@ +from pandas import DataFrame +from typing import Optional + +def dropUpToFeature(dataframe:DataFrame, + feature_name:str, + keep_feature_name_column:Optional[bool] = False + ): + """ Function to drop all columns up to and possibly including the specified feature. + + Parameters + ---------- + dataframe : DataFrame + Dataframe to drop columns from. + feature_name : str + Name of the feature to drop up to. + keep_feature_name_column : bool, optional + Whether to keep the specified feature name column in the dataframe or drop it. The default is False. + + Returns + ------- + dataframe : DataFrame + Dataframe with all columns up to and including the specified feature dropped. + """ + try: + if keep_feature_name_column: + # Get the column names up to but not including the specified feature + column_names = dataframe.columns.to_list()[:dataframe.columns.get_loc(feature_name)] + else: + # Get the column names up to and including the specified feature + column_names = dataframe.columns.to_list()[:dataframe.columns.get_loc(feature_name)+1] + + # Drop all columns up to and including the specified feature + dataframe_dropped_columns = dataframe.drop(columns=column_names) + + return dataframe_dropped_columns + + except KeyError: + print(f"Feature {feature_name} was not found as a column in dataframe. No columns dropped.") + return dataframe + + except Exception as e: + print(f"An error occurred: {e}") + return None \ No newline at end of file From fe5625792bea029eb40398f77aaad99d590ff2ba Mon Sep 17 00:00:00 2001 From: Katy Scott Date: Fri, 6 Dec 2024 16:21:36 -0500 Subject: [PATCH 16/16] fix: set continuous setting in StructureSetToSegmentation to False --- src/readii/loaders.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/readii/loaders.py b/src/readii/loaders.py index 690e660..ac1aedc 100644 --- a/src/readii/loaders.py +++ b/src/readii/loaders.py @@ -72,7 +72,11 @@ def loadRTSTRUCTSITK( # Set up segmentation loader logger.debug(f"Making mask using ROI names: {roiNames}") - makeMask = StructureSetToSegmentation(roi_names=roiNames) + + # Initialize med-imagetools loader to convert RTSTRUCT point cloud to a segmentation + # Set continous to False to ensure indices are integers and not floats + makeMask = StructureSetToSegmentation(roi_names=roiNames, + continuous=False) try: # Get the individual ROI masks