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Saving analysis outputs in folders according to SWC-Blueprint (#60)
Co-authored-by: Niko Sirmpilatze <[email protected]>
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@@ -30,6 +30,7 @@ dependencies = [ | |
| "scipy", | ||
| "numba", | ||
| "tqdm", | ||
| "GitPython", | ||
| ] | ||
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|
||
| [project.urls] | ||
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|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,240 @@ | ||
| from pathlib import Path | ||
| from typing import Union | ||
|
|
||
| from rsp_vision.objects.folder_naming_specs import FolderNamingSpecs | ||
|
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|
|
||
| class SWC_Blueprint_Spec: | ||
| def __init__( | ||
| self, | ||
| project_name: str, | ||
| raw_data: bool = False, | ||
| derivatives: bool = True, | ||
| local_path: Path = Path().absolute(), | ||
| ) -> None: | ||
| """ | ||
| Create a `SWC_Blueprint_Spec` object to specify the location of the | ||
| raw data and/or derivatives for a project. | ||
| Please refer to https://swc-blueprint.neuroinformatics.dev/ for more | ||
| information about SWC Blueprint. | ||
| Parameters | ||
| ---------- | ||
| project_name : str | ||
| The name of the project folder. | ||
| raw_data : bool, optional | ||
| Whether you want to create a subfolder for raw data or not, | ||
| by default False. | ||
| derivatives : bool, optional | ||
| Whether you want to create a subfolder for derivatives or not, | ||
| by default True. | ||
| local_path : Path, optional | ||
| The path to the local folder where you want to create the project, | ||
| by default Path().absolute(). | ||
| """ | ||
| self.project_name = project_name | ||
| self.raw_data = raw_data | ||
| self.derivatives = derivatives | ||
| self.path = ( | ||
| local_path / self.project_name / "derivatives" | ||
| if derivatives | ||
| else local_path / self.project_name / "raw_data" | ||
| ) | ||
| self.logs_path = local_path / self.project_name / "logs" | ||
|
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||
|
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||
| class SubjectFolder: | ||
| """ | ||
| A class to represent a subject folder in SWC Blueprint. | ||
| This specific implementation is for the rsp_vision project. | ||
| The subject folder will have the following format: | ||
| sub-###_line-###_id-### (e.g. sub-001_line-C57_id-123). | ||
| Line and id are specified in the `FolderNamingSpecs` object or | ||
| in the table row. The table is a pandas DataFrame that contains | ||
| the information about the subject that were already analysed. | ||
| Attributes | ||
| ---------- | ||
| swc_blueprint_spec : SWC_Blueprint_Spec | ||
| The SWC Blueprint specification for the project. | ||
| sub_num : int | ||
| The subject number. | ||
| sub_folder_name : str | ||
| The name of the subject folder. It contains the subject number, | ||
| the mouse line and the mouse id. | ||
| sub_folder_path : Path | ||
| The path to the subject folder. | ||
| Methods | ||
| ------- | ||
| make_from_folder_naming_specs(folder_naming_specs, sub_num) | ||
| Create a `SubjectFolder` object from a `FolderNamingSpecs` object | ||
| and a subject number. | ||
| make_from_table_row(table_row) | ||
| Create a `SubjectFolder` object from a row of a table (a dict which | ||
| corresponds to a row of the "analysis_log.csv" file). | ||
| Raises | ||
| ------ | ||
| ValueError | ||
| If the argument `folder_or_table` is neither 'folder' nor 'table'. | ||
| """ | ||
|
|
||
| def __init__( | ||
| self, | ||
| swc_blueprint_spec: SWC_Blueprint_Spec, | ||
| folder_or_table: Union[FolderNamingSpecs, dict], | ||
| sub_num: int, | ||
| ): | ||
| self.swc_blueprint_spec = swc_blueprint_spec | ||
| if isinstance(folder_or_table, FolderNamingSpecs): | ||
| self.make_from_folder_naming_specs(folder_or_table, sub_num) | ||
| elif isinstance(folder_or_table, dict): | ||
| self.make_from_table_row(folder_or_table) | ||
| else: | ||
| raise ValueError( | ||
| "The argument `folder_or_table` must be an instance of " | ||
| + "`FolderNamingSpecs` or a dictionary." | ||
| ) | ||
| self.sub_folder_path = Path( | ||
| self.swc_blueprint_spec.path / self.sub_folder_name | ||
| ) | ||
|
|
||
| def make_from_folder_naming_specs( | ||
| self, | ||
| folder_naming_specs: FolderNamingSpecs, | ||
| sub_num: int, | ||
| ): | ||
| self.sub_num = sub_num | ||
| self.sub_folder_name = ( | ||
| f"sub-{sub_num:03d}" | ||
| + "_line-" | ||
| + folder_naming_specs.mouse_line | ||
| + "_id-" | ||
| + folder_naming_specs.mouse_id | ||
| ) | ||
|
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||
| def make_from_table_row(self, table_row: dict): | ||
| self.sub_num = int(table_row["sub"]) | ||
| self.sub_folder_name = ( | ||
| f"sub-{self.sub_num:03d}" | ||
| + "_line-" | ||
| + table_row["mouse_line"] | ||
| + "_id-" | ||
| + str(table_row["mouse_id"]) | ||
| ) | ||
|
|
||
|
|
||
| class SessionFolder: | ||
| """ | ||
| A class to represent a session folder in SWC Blueprint. | ||
| This specific implementation is for the rsp_vision project. | ||
| The session folder will have the following format: | ||
| ses-###_hemisphere-###_region-###_monitor-###_fov-###_cre-### (e.g. | ||
| ses-000_hemisphere-hL_region-RSPd_monitor-front); | ||
| `fov` and `cre` are optional. | ||
| Attributes | ||
| ---------- | ||
| subject_folder : SubjectFolder | ||
| The subject folder. | ||
| ses_num : int | ||
| The session number. | ||
| monitor : str | ||
| The monitor position. | ||
| ses_folder_name : str | ||
| The name of the session folder. It contains the session number, | ||
| the hemisphere, the brain region, the monitor position, the field | ||
| of view and the cre line (if applicable). | ||
| ses_folder_path : Path | ||
| The path to the session folder. | ||
| Methods | ||
| ------- | ||
| make_from_folder_naming_specs(folder_naming_specs, ses_num) | ||
| Create a `SessionFolder` object from a `FolderNamingSpecs` object | ||
| and a session number. | ||
| make_from_table_row(table_row) | ||
| Create a `SessionFolder` object from a table row. | ||
| Raises | ||
| ------ | ||
| ValueError | ||
| If the argument `folder_or_table` is neither 'folder' nor 'table'. | ||
| """ | ||
|
|
||
| def __init__( | ||
| self, | ||
| subject_folder: SubjectFolder, | ||
| folder_or_table: Union[FolderNamingSpecs, dict], | ||
| ses_num: int, | ||
| ): | ||
| self.subject_folder = subject_folder | ||
| if isinstance(folder_or_table, FolderNamingSpecs): | ||
| self.make_from_folder_naming_specs(folder_or_table, ses_num) | ||
| elif isinstance(folder_or_table, dict): | ||
| self.make_from_table_row(folder_or_table) | ||
| else: | ||
| raise ValueError( | ||
| "The argument `folder_or_table` must be an instance of " | ||
| + "`FolderNamingSpecs` or a dictionary." | ||
| ) | ||
| self.ses_folder_path = Path( | ||
| self.subject_folder.sub_folder_path / self.ses_folder_name | ||
| ) | ||
|
|
||
| def make_from_folder_naming_specs( | ||
| self, | ||
| folder_naming_specs: FolderNamingSpecs, | ||
| ses_num: int, | ||
| ): | ||
| self.ses_num = ses_num | ||
| self.monitor = ( | ||
| "_".join(folder_naming_specs.monitor_position.split("_")[1:]) | ||
| .replace("_", "-") | ||
| .replace("-", "") | ||
| ) | ||
| self.ses_folder_name = ( | ||
| f"ses-{self.ses_num:03d}" | ||
| + "_hemisphere-" | ||
| + folder_naming_specs.hemisphere | ||
| + "_region-" | ||
| + folder_naming_specs.brain_region | ||
| + "_monitor-" | ||
| + self.monitor | ||
| + ( | ||
| "_fov-" + folder_naming_specs.fov | ||
| if folder_naming_specs.fov | ||
| else "" | ||
| ) | ||
| + ( | ||
| "_cre-" + folder_naming_specs.cre | ||
| if folder_naming_specs.cre | ||
| else "" | ||
| ) | ||
| ) | ||
|
|
||
| def make_from_table_row(self, table_row: dict): | ||
| self.ses_num = int(table_row["ses"]) | ||
| self.monitor = table_row["monitor_position"] | ||
| self.ses_folder_name = ( | ||
| f"ses-{self.ses_num:03d}" | ||
| + "_hemisphere-" | ||
| + table_row["hemisphere"] | ||
| + "_region-" | ||
| + table_row["brain_region"] | ||
| + "_monitor-" | ||
| + self.monitor | ||
| + ( | ||
| "_fov-" + str(table_row["fov"]) | ||
| if (str(table_row["fov"]) != "nan") | ||
| else "" | ||
| ) | ||
| + ( | ||
| "_cre-" + str(table_row["cre"]) | ||
| if (str(table_row["cre"]) != "nan") | ||
| else "" | ||
| ) | ||
| ) |
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