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class
BaseRecon(name='BaseRecon')[source] -
base_pre_process()[source] This method is called after the plugin has been created by the pipeline framework as a pre-processing step.
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base_process_frames_after(data)[source] This method is called directly after each call to process frames and before returning the data to file.
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base_process_frames_before(data)[source] Reconstruct a single sinogram with the provided centre of rotation
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br_array_pad(ctr, nPixels)[source]
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crop_sino(sino, cor)[source] Crop the sinogram so the centre of rotation is at the centre.
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executive_summary()[source] Provide a summary to the user for the result of the plugin.
- e.g.
Warning, the sample may have shifted during data collection
Filter operated normally
- Returns
A list of string summaries
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get_angles()[source] Get the angles associated with the current sinogram(s).
- Returns
Angles of the current frames.
- Return type
np.ndarray
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get_centre_offset(sino, cor, detX)[source]
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get_centre_shift(sino, cor)[source]
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get_cors()[source] Get the centre of rotations associated with the current sinogram(s).
- Returns
Centre of rotation values for the current frames.
- Return type
np.ndarray
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get_fov_fraction(sino, cor)[source] Get the fraction of the original FOV that can be reconstructed due to offset centre
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get_frame_params()[source]
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get_frame_shifts()[source]
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get_gpu_memory()[source]
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get_initial_data()[source] Get the initial data (if it is exists) associated with the current sinogram(s).
- Returns
The section of the initialisation data associated with the current frames.
- Return type
np.ndarray or None
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get_max_frames()[source] Number of data frames to pass to each instance of process_frames func
- Returns
- “single”, “multiple” or integer (only to be used if the number of
frames MUST be fixed.)
- Return type
str or int
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get_pad_amount()[source]
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get_proj_shifts()[source] Get the 2D (X-Y) shifts associated with every projection frame
- Returns
projecton shifts for the current frames.
- Return type
np.ndarray
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get_reconstruction_alg()[source]
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get_sino_centre_method()[source]
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get_skipping_indices(in_text)[source]
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get_slice_axis()[source] Fix the fastest changing slice dimension
- Returns
str should be the axis_label corresponding to the fastest changing dimension
- Return type
str or None
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get_vol_shape()[source]
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keep_sino(sino, cor)[source] No change to the sinogram
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nInput_datasets()[source] The number of datasets required as input to the plugin
- Returns
Number of input datasets
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nOutput_datasets()[source] The number of datasets created by the plugin
- Returns
Number of output datasets
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pad_sino(sino, cor)[source] Pad the sinogram so the centre of rotation is at the centre.
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populate_metadata_to_output(inData, outData, mData, meta_list)[source]
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reconstruct_pre_process()[source] Should be overridden to perform pre-processing in a child class
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set_centre_of_rotation(inData, outData, mData)[source]
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set_function(pad_shape)[source]
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set_mask(shape)[source]
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set_projection_shifts(inData, outData, mData)[source]
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setup()[source] This method is first to be called after the plugin has been created. It determines input/output datasets and plugin specific dataset information such as the pattern (e.g. sinogram/projection).
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