This repository has been archived by the owner on Oct 30, 2024. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Saving analysis outputs in folders according to SWC-Blueprint (#60)
Co-authored-by: Niko Sirmpilatze <[email protected]>
- Loading branch information
1 parent
a0d5054
commit a3d1916
Showing
12 changed files
with
1,120 additions
and
63 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -30,6 +30,7 @@ dependencies = [ | |
| "scipy", | ||
| "numba", | ||
| "tqdm", | ||
| "GitPython", | ||
| ] | ||
|
|
||
| [project.urls] | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | ||
|
|
||
|
|
||
| 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" | ||
|
|
||
|
|
||
| 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 | ||
| ) | ||
|
|
||
| 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 "" | ||
| ) | ||
| ) |
Oops, something went wrong.