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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| import os | ||
| from imlib.general.system import ensure_directory_exists | ||
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| class NiftyRegPaths: | ||
| def __init__(self, niftyreg_directory): | ||
| self.niftyreg_directory = niftyreg_directory | ||
| ensure_directory_exists(self.niftyreg_directory) | ||
| self.niftyreg_process_directory = os.path.join( | ||
| niftyreg_directory, "process" | ||
| ) | ||
| ensure_directory_exists(self.niftyreg_process_directory) | ||
| self.make_reg_paths() | ||
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| def make_reg_paths(self): | ||
| self.downsampled_brain = self.make_reg_path("downsampled.nii") | ||
| self.downsampled_brain_standard_space = self.make_reg_path( | ||
| "downsampled_standard.nii" | ||
| ) | ||
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| self.brain_filtered = self.make_reg_path("brain_filtered.nii") | ||
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| self.hemispheres = self.make_reg_path("hemispheres.nii") | ||
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| self.annotations = self.make_reg_path("annotations.nii") | ||
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| self.downsampled_filtered = self.make_reg_path( | ||
| "downsampled_filtered.nii" | ||
| ) | ||
| self.registered_atlas_path = self.make_reg_path("registered_atlas.nii") | ||
| self.hemispheres_atlas_path = self.make_reg_path( | ||
| "registered_hemispheres.nii" | ||
| ) | ||
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| self.affine_registered_atlas_brain_path = self.make_reg_path( | ||
| "affine_registered_atlas_brain.nii" | ||
| ) | ||
| self.freeform_registered_atlas_brain_path = self.make_reg_path( | ||
| "freeform_registered_atlas_brain.nii" | ||
| ) | ||
| self.inverse_freeform_registered_atlas_brain_path = self.make_reg_path( | ||
| "inverse_freeform_registered_brain.nii" | ||
| ) | ||
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| self.registered_atlas_img_path = self.make_reg_path( | ||
| "registered_atlas.nii" | ||
| ) | ||
| self.registered_hemispheres_img_path = self.make_reg_path( | ||
| "registered_hemispheres.nii" | ||
| ) | ||
|
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| self.affine_matrix_path = self.make_reg_path("affine_matrix.txt") | ||
| self.invert_affine_matrix_path = self.make_reg_path( | ||
| "invert_affine_matrix.txt" | ||
| ) | ||
|
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| self.control_point_file_path = self.make_reg_path( | ||
| "control_point_file.nii" | ||
| ) | ||
| self.inverse_control_point_file_path = self.make_reg_path( | ||
| "inverse_control_point_file.nii" | ||
| ) | ||
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| self.deformation_field = self.make_reg_path("deformation_field.nii") | ||
| ( | ||
| self.deformation_log_file_path, | ||
| self.deformation_error_file_path, | ||
| ) = self.compute_reg_log_file_paths("deformation") | ||
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||
| ( | ||
| self.affine_log_file_path, | ||
| self.affine_error_path, | ||
| ) = self.compute_reg_log_file_paths("affine") | ||
| ( | ||
| self.freeform_log_file_path, | ||
| self.freeform_error_file_path, | ||
| ) = self.compute_reg_log_file_paths("freeform") | ||
| ( | ||
| self.inverse_freeform_log_file_path, | ||
| self.inverse_freeform_error_file_path, | ||
| ) = self.compute_reg_log_file_paths("inverse_freeform") | ||
| ( | ||
| self.segmentation_log_file, | ||
| self.segmentation_error_file, | ||
| ) = self.compute_reg_log_file_paths("segment") | ||
| ( | ||
| self.inverse_transform_log_file, | ||
| self.inverse_transform_error_file, | ||
| ) = self.compute_reg_log_file_paths("inverse_transform") | ||
| ( | ||
| self.invert_affine_log_file, | ||
| self.invert_affine_error_file, | ||
| ) = self.compute_reg_log_file_paths("invert_affine") | ||
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| def make_reg_path(self, basename): | ||
| """ | ||
| Compute the absolute path of the destination file to | ||
| self.registration_output_folder. | ||
| :param str basename: | ||
| :return: The path | ||
| :rtype: str | ||
| """ | ||
| return os.path.join(self.niftyreg_process_directory, basename) | ||
|
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| def compute_reg_log_file_paths(self, basename): | ||
| """ | ||
| Compute the path of the log and err file for the step corresponding | ||
| to basename | ||
| :param str basename: | ||
| :return: log_file_path, error_file_path | ||
| """ | ||
|
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| log_file_template = os.path.join( | ||
| self.niftyreg_process_directory, "{}.log" | ||
| ) | ||
| error_file_template = os.path.join( | ||
| self.niftyreg_process_directory, "{}.err" | ||
| ) | ||
| log_file_path = log_file_template.format(basename) | ||
| error_file_path = error_file_template.format(basename) | ||
| return log_file_path, error_file_path |
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