Source code for sas.sascalc.file_converter.bsl_loader

import os

import numpy as np

from ..dataloader.data_info import Data2D

[docs]class BSLParsingError(Exception): pass
[docs]class BSLLoader: """ Loads 2D SAS data from a BSL file. CLoader is a C extension (found in c_ext/bsl_loader.c) See http://www.diamond.ac.uk/Beamlines/Soft-Condensed-Matter/small-angle/SAXS-Software/CCP13/BSL.html for more info on the BSL file format. """ def __init__(self, filename): """ Parses the BSL header file and sets instance variables apropriately :param filename: Path to the BSL header file """ [folder, filename] = os.path.split(filename) sasdata_filename = filename.replace('000.', '001.') if sasdata_filename == filename: err_msg = ("Invalid header filename {}.\nShould be of the format " "Xnn000.XXX where X is any alphanumeric character and n is any" " digit.").format(filename) raise BSLParsingError(err_msg) data_info = {} with open(os.path.join(folder, filename), 'r') as header_file: data_info = self._parse_header(header_file, filename, sasdata_filename, folder) self.filename = data_info['filename'] self.n_frames = data_info['frames'] self.n_pixels = data_info['pixels'] self.n_rasters = data_info['rasters'] self.swap_bytes = data_info['swap_bytes'] def _parse_header(self, header_file, filename, sasdata_filename, folder): """ Method that parses the header file and returns the metadata in data_info :param header_file: header file object. :return: metadata of header file. """ data_info = {} # First 2 lines are headers header_file.readline() header_file.readline() metadata = header_file.readline().strip() metadata = metadata.split() data_filename = header_file.readline().strip() if len(metadata) != 10: err_msg = "Invalid header file: {}".format(filename) raise BSLParsingError(err_msg) if data_filename != sasdata_filename: last_file = (metadata[9] == '0') if last_file: # Reached last file we have metadata for err_msg = "No metadata for {} found in header file: {}" err_msg = err_msg.format(sasdata_filename, filename) raise BSLParsingError(err_msg) try: data_info = { 'filename': os.path.join(folder, data_filename), 'pixels': int(metadata[0]), 'rasters': int(metadata[1]), 'frames': int(metadata[2]), 'swap_bytes': int(metadata[3]) } except Exception: err_msg = "Invalid metadata in header file for {}" err_msg = err_msg.format(sasdata_filename) raise BSLParsingError(err_msg) return data_info @property def filename(self): """ File to load. """ return self._filename @filename.setter def filename(self, filename): self._filename = str(filename) @property def n_frames(self): """ Number of frames in the file. """ return self._n_frames @n_frames.setter def n_frames(self, n_frames): self._n_frames = int(n_frames) @property def n_pixels(self): """ Number of pixels in the file. """ return self._n_pixels @n_pixels.setter def n_pixels(self, n_pixels): self._n_pixels = int(n_pixels) @property def n_rasters(self): """ Number of rasters in the file. """ return self._n_rasters @n_rasters.setter def n_rasters(self, n_rasters): self._n_rasters = int(n_rasters) @property def swap_bytes(self): """ Whether or not the bytes are in reverse order. """ return self._swap_bytes @swap_bytes.setter def swap_bytes(self, swap_bytes): self._swap_bytes = bool(swap_bytes)
[docs] def load_frames(self, frames): """ Loads all frames of the BSl file into a Data2D object. :param frames: Number of frames. :return: Data2D frame_data. """ frame_data = [] # Prepare axis values (arbitrary scale) x = self.n_rasters * list(range(1, self.n_pixels+1)) y = [self.n_pixels * [i] for i in list(range(1, self.n_rasters+1))] y = np.reshape(y, (1, self.n_pixels*self.n_rasters))[0] x_bins = x[:self.n_pixels] y_bins = y[0::self.n_pixels] for frame in frames: raw_frame_data = self.load_data(frame) data2d = Data2D(data=raw_frame_data, qx_data=x, qy_data=y) data2d.x_bins = x_bins data2d.y_bins = y_bins data2d.Q_unit = '' # Using arbitrary units frame_data.append(data2d) return frame_data
[docs] def load_data(self, frame): """ Loads the file named in filename in 4 byte float, in either little or big Endian depending on self.swap_bytes. :param frame: The frame to load. :return: np array of loaded floats. """ # Set dtype to 4 byte float, big or little endian depending on swap_bytes. dtype = ('>f4', '<f4')[self.swap_bytes] # Size of float as stored in binary file should be 4 bytes. float_size = 4 offset = self.n_pixels * self.n_rasters * frame * float_size with open(self.filename, 'rb') as input_file: input_file.seek(offset) # CRUFT: With numpy 1.17, could use np.fromfile(self.filename, dtype=dtype, offset=offset). data = np.float64(np.fromfile(input_file, dtype=dtype)) return data
def __str__(self): """ Print the objects params. :return: string description of object parameters. """ desc = "Filename: " + self.filename + "\n" desc += "n_frames: " + str(self.n_frames) + "\n" desc += "n_pixels: " + str(self.n_pixels) + "\n" desc += "n_rasters: " + str(self.n_rasters) + "\n" desc += "swap_bytes: " + str(self.swap_bytes) + "\n" return desc