Merge pull request INT-NIT#163 from sifaoufatai/microscopy-confocal

Microscopy confoncal and eyetracking customization parts

Author: dumaatravaie

.gitignore

@@ -58,4 +58,4 @@ Thumbs.db
 # Fichiers temporaires à ignorer
 BIDSTools/dev_tests/fff.json
 BIDSTools/dev_tests/ffffff.json
-BIDSTools/dev_tests/fff.CSV
+bep032tools/fff.CSV

BIDSTools/BIDS_PROJECT_CONFIG/BIDS_modality_custom.py

@@ -0,0 +1,356 @@
+"""
+bids_modality_custom.py
+this file contain contain the common modlity custom part of bids project
+and the customieation  part of each modlity
+it is a factory for  creating custom modality classes which will process the data , with the good  format and
+the good path ( here is the place for the conversion part)
+the current directory is the directory where the BIDS output will be written
+example:
+
+  /sub-1/session-1/beh/  #  as current directory
+        sub_1_session_1_beh_task-1-events.tsv   # as data file  writin in the current directory
+        sub_1_session_1_beh_task-1-eyetracking.tsv # as data file  writin in the current directory
+
+
+
+
+"""
+from BIDSTools.ProjectConfig import ProjectConfig
+from BIDSTools.Experiment import Experiment
+import os
+import shutil
+from BIDSTools.convertfileformat import ConvertedfSData
+from BIDSTools.log import  log
+class BIDSCommonModality:
+    def __init__(self, project_config, experiment, current_dir,converter = None):
+        """
+        Initialize the BIDSCommonModality class with project configuration, experiment details, and directory path.
+
+        Parameters
+        ----------
+        project_config : ProjectConfig
+            An instance of the ProjectConfig class containing project-specific configurations.
+        experiment : Experiment
+            An instance of the Experiment class containing details of the current experiment.
+        current_dir : str
+            Path to the current working directory where files will be processed and stored.
+        converter : optional
+            An optional converter object for handling data format conversions.
+
+        Attributes
+        ----------
+        segment_type : str
+            The type of segment (e.g., 'run', 'chunk') as defined in the project configuration.
+        segment_id_attr : str
+            The attribute name for segment IDs, formatted based on segment type.
+        data_type : str
+            The data type as specified in the project configuration.
+        segment_list : list
+            A list of segments obtained from the project configuration.
+        data_file_format : str
+            The file format pattern for data files as defined in the project configuration.
+        custom_pattern : str
+            The custom configuration pattern for segments.
+        segment_dict : dict
+            A dictionary to store segment details.
+        converter : optional
+            An optional converter object for handling data format conversions.
+        """
+        self.project_config = project_config
+        self.experiment = experiment
+        self.current_dir = current_dir
+        self.segment_type = self.project_config.get_segement_value()  # e.g., 'run', 'chunk', etc.
+        self.segment_id_attr = self.project_config.config.get('segment_id', f"{self.segment_type}_id").format(segment=self.segment_type)
+        self.data_type =self.project_config.get_data_type()
+        self.segment_list = self.project_config.get_segments_list()
+        self.data_file_format = self.project_config.get_data_file_format()
+        self.custom_pattern = self.project_config.get_custom_config()
+        self.segment_dict = {}
+        self.converter = converter
+
+    def get_segment_details(self):
+        segment_dict = {}
+        experiment_dict = self.experiment.to_dict()
+
+        for segment_key in self.segment_list:
+            segment_data = {}
+
+
+            # Find all fields in the experiment that start with this segment_key
+            segment_fields = [
+                field_name.replace(f"{segment_key}_", "")
+                for field_name in experiment_dict
+                if field_name.startswith(f"{segment_key}_")
+            ]
+            print(segment_fields)
+            for field in segment_fields:
+
+                pattern = self.custom_pattern.format(
+                    **{f"{self.segment_type}_key": segment_key, "field": field, "segment_key": segment_key}
+                )
+                value = getattr(self.experiment, pattern, None)
+                segment_data[field] = value
+
+            segment_data[self.segment_type] = segment_key
+
+            raw_data_path_pattern = self.project_config.get_raw_data_path()
+
+            print("format dict:", {f"{self.segment_type}_key": segment_key,
+                                   "segment_key": segment_key})
+            segment_data['raw_data_path'] = getattr(
+                self.experiment,
+                raw_data_path_pattern.format(**{f"{self.segment_type}_key": segment_key, "segment_key": segment_key}),
+                None
+            )
+            print(segment_data)
+            # Add segment_id if available
+            if 'id' in segment_data:
+                segment_data[self.segment_id_attr] = segment_data['id']
+                segment_data['segment_id'] = segment_data['id']
+            else:
+                raise ValueError(f"Segment ID not found for {segment_key}")
+
+
+
+            segment_dict[segment_key] = segment_data
+            self.segment_dict = segment_dict
+        return segment_dict
+
+    def get_segment_data_path(self, segment):
+        # Add any extra info from experiment or segment
+
+
+        """
+        Formats the data path for a given segment based on the BIDS configuration.
+
+        Parameters
+        ----------
+        segment : dict
+            A dictionary containing information about the segment.
+
+        Returns
+        -------
+        segment : dict
+            The input dictionary with an additional 'final_path' key containing the formatted data path.
+        """
+
+        segment_info = self.experiment.to_dict()
+        segment_info.update(segment)
+
+        segment_info['modality'] = self.project_config.global_config.get('modality', 'unknown')
+
+        segment['final_path'] = self.data_file_format.format(**segment_info)
+
+        return segment
+
+    def write_segment_info(self):
+        """
+        Write BIDS segment information files for the experiment.
+
+        Copies raw data for each segment to the correct location if available.
+        Creates a converter for each segment if available and calls its convert_bids_data method.
+        """
+        details = self.get_segment_details()
+        for segment_key, segment_info in details.items():
+            segment_info = self.get_segment_data_path(segment_info)
+            # create empty file with final path
+            os.makedirs(self.current_dir, exist_ok=True)
+           # with open(os.path.join(self.current_dir, segment_info['final_path']), 'w') as f:
+            #    f.write('')
+            # copy raw data if available to  destination path with the correct name
+
+            if segment_info.get('raw_data_path'):
+                # this will copy the raw data to the current directory
+                shutil.copyfile(
+                    segment_info['raw_data_path'],
+                    os.path.join(self.current_dir, os.path.basename(segment_info['final_path'])),
+                )
+                final_raw_data_path = os.path.join(self.current_dir, os.path.basename(segment_info['final_path']))
+                segment_info['final_raw_data_path'] = final_raw_data_path
+                # creat the specific converter with segment info
+                self.create_converter(segment_info)
+                if self.converter is None:
+
+                    log.info(f"Modality {self.project_config.global_config.get('modality')} has no converter")
+
+
+                else:
+
+
+
+                    # make the conversion if the converter is  available
+
+                    self.converter.convert_bids_data()
+
+
+
+
+
+
+    def create_converter(self, segment_info):
+        """
+        Creates a converter for the given segment_info.
+
+        Parameters
+        ----------
+        segment_info : dict
+            A dictionary containing information about the segment.
+
+        Notes
+        -----
+        The converter is determined by the file extension of the raw data path in the segment info.
+        Currently, only .edf files are supported and use the `ConvertedfSData` converter.
+        """
+        raw_data_path = segment_info['raw_data_path']
+        all_info = self.experiment.to_dict()
+        all_info.update(segment_info)
+        temps_exp=Experiment(**all_info)
+        ext = os.path.splitext(raw_data_path)[1]
+        final_raw_data_path = segment_info['final_raw_data_path']
+
+
+
+
+
+        if ext=='.edf':
+           self.converter = ConvertedfSData(final_raw_data_path, None, self.current_dir, temps_exp)
+
+
+        else:
+            log.info(f"Unknown file format: {ext}")
+
+
+
+
+
+
+
+
+
+
+class MicroscopyCustom(BIDSCommonModality):
+    def __init__(self, project_config, experiment, current_dir):
+        """
+        Initialize the MicroscopyCustom class.
+
+        Parameters
+        ----------
+        project_config : ProjectConfig
+            The project configuration object.
+        experiment : Experiment
+            The experiment object.
+        current_dir : str
+            The directory where the BIDS output will be written.
+
+        Notes
+        -----
+        This class is a customization of the BIDSCommonModality class for Microscopy projects.
+        It sets the microscope_type attribute of the experiment to the value in the project config.
+        """
+        super().__init__(project_config, experiment, current_dir)
+        self.microscopy_type =self.project_config.global_config.get('microscope_type', 'CONF')
+        experiment.microscope_type = self.microscopy_type
+
+
+class EyetrackingCustom(BIDSCommonModality):
+    def __init__(self, project_config, experiment, current_dir):
+        """
+        Initialize the EyetrackingCustom class.
+
+        Parameters
+        ----------
+        project_config : ProjectConfig
+            The project configuration object.
+        experiment : Experiment
+            The experiment object.
+        current_dir : str
+            The directory where the BIDS output will be written.
+
+        Notes
+        -----
+        This class is a customization of the BIDSCommonModality class for Eyetracking projects.
+        """
+        super().__init__(project_config, experiment, current_dir)
+        super().__init__(project_config, experiment, current_dir)
+
+
+
+
+class ModalityCustomBuilder:
+    def __init__(self, project_config, experiment, current_dir):
+        """
+        Initialize the ModalityCustomBuilder class.
+
+        Parameters
+        ----------
+        project_config : ProjectConfig
+            The project configuration object.
+        experiment : Experiment
+            The experiment object.
+        current_dir : str
+            The directory where the BIDS output will be written.
+
+        Notes
+        -----
+        This class is a factory for creating custom modality classes based on the project configuration.
+        It creates an instance of either the MicroscopyCustom or EyetrackingCustom class depending on the project name.
+        """
+        if project_config.get_project_name() == 'microscopy_confocal':
+            self.custom = MicroscopyCustom(project_config, experiment, current_dir)
+        elif project_config.get_project_name() == 'eyetracking':
+            self.custom = EyetrackingCustom(project_config, experiment, current_dir)
+        else:
+            raise ValueError(f"Unknown project config: {project_config.get_project_name()} perhaps check your config file?")
+
+    def build_customizations(self):
+        self.custom.write_segment_info()
+        return self.custom
+
+
+
+if __name__ == "__main__":
+    from BIDSTools.ProjectConfig import ProjectConfig
+    from BIDSTools.Experiment import Experiment
+
+    # Example: Load config and create a mock experiment
+    config_file = "/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/BIDS_PROJECT_CONFIG/microscopy_confocal.yml"
+    config_file2 = "/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/BIDS_PROJECT_CONFIG/eyetracking.yml"
+    project_config = ProjectConfig(config_file)
+    project_config2 = ProjectConfig(config_file2)
+
+    # Mock experiment with fields for 2 segments
+    experiment = Experiment(
+        participant_id="001",
+        session_id="01",
+        modality="eyetracking",
+        task="test",
+        sample_id="01",
+        imageo01_datafile_path="/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/data/im0.czi",
+        image01_id="01",
+        image01_datafile_path="/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/data/im0.czi",
+        image02_id="02"
+
+    )
+    experiment2 = Experiment(
+        participant_id="01",
+        session_id="01",
+        task="test",
+        modality="eyetracking",
+        run01_datafile_path="/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/data/im0.czi",
+        run01_id="01",
+        run02_datafile_path="/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/data/im0.czi",
+        run02_id="02",
+        run03_datafile_path="/home/INT/idrissou.f/PycharmProjects/BEP032tools/BIDSTools/data/im0.czi",
+        run03_id="03"
+    )
+    output_dir = "./output"
+
+
+    # use  common parent class
+    #handler = BIDSCommonModality(project_config, experiment, output_dir)
+    #handler = BIDSCommonModality(project_config2, experiment2, output_dir)
+    # use custom classes
+    handler= MicroscopyCustom(project_config, experiment, output_dir)
+    #handler= EyetrackingCustom(project_config2, experiment2, output_dir)
+
+    handler.write_segment_info()