wedgeutils#

cryocat.utils.wedgeutils.apply_wedge_mask(wedge_mask, in_map, rotation_zxz=None, output_path=None)#

cryocat.utils.wedgeutils.check_data_consistency(data1, data2, data_type1, data_type2)#

Check the consistency of two sets of data.

Parameters:

data1numpy.ndarray: The first set of data.
data2numpy.ndarray: The second set of data.
data_type1str: The type of data in data1.
data_type2str: The type of data in data2.

Returns:

None: This function does not return anything.

Raises:

TypeError: If data1 or data2 isn’t numpy.ndarray type.
ValueError: If the number of entries in data1 is different from the number of entries in data2.

cryocat.utils.wedgeutils.create_wedge_list_em_batch(tomo_list, tlt_file_format, output_file=None)#

Create a wedge list dataframe in EM format for all tomograms/tilt series specified in tomo_list.

Parameters:

tomo_liststr or array-like: The path to the file containing list of tomograms (txt) or tomogram/tilt series numbers specified as array-like variable. See cryocat.ioutils.tlt_load() for more information on formatting.
tlt_file_formatstr: The format describing name of the input files (including the path) with tilt angles. See Notes below for more information. See cryocat.ioutils.tlt_load() for more information on allowed input files (tlt, mdoc, xml).
output_filestr, optional: The path to the output file, by default None. If None, the output is not written out.

Returns:

pandas.DataFrame: The wedge list dataframe in EM format for all tomograms/tilt series specified by tomo_list.

See also

cryocat.ioutils.tlt_load()

Notes

The variables with _file_format in name should contain pattern that will be replaced by tomogram/tilt series numbers specified in the tomo_list. The pattern should start with $ and should be followed by sequnece of x. The sequence of x will be replaced by tomogram/tilt series number from tomo_list and pad with zeros if necessary. For example, if tlt_file_format is specified as “TS_$xxx/$xxx.tlt” and the tomo_list contains numbers 79 and 155, the final file names will be TS_079/079.tlt and TS_155/155.tlt. The sequence of x can be of arbitrary length, even within one file format, e.g. “TS_$xxxx/$xxx.tlt”. However, the minimal allowed length of the sequence is given by the number of digits of the largest tomogram/tilt series number. For instance, TS_$xx/$xxx.tlt will fail since tomogram 155 requires sequence of at least 3 x. It is expected that all files of the same type will follow same formatting. Different file types can follow different formatting. For example, the tlt_file_format can be TS_$xxx/$xxx.tlt but defocus files can be all in one folder specified as “ctf_files/$xxxx_ctffind4.txt”.

cryocat.utils.wedgeutils.create_wedge_list_sg(tomo_id, tomo_dim, pixel_size, tlt_file, z_shift=0.0, ctf_file=None, ctf_file_type='gctf', dose_file=None, voltage=300.0, amp_contrast=0.07, cs=2.7, output_file=None, drop_nan_columns=True)#

Create a wedge list dataframe for a single tomogram/tilt series in STOPGAP format.

Parameters:

tomo_idint: The ID of the tomogram.
tomo_dimstr or array-like: The path to the tomogram dimensions file or dimensions specified as array-like variable. See cryocat.ioutils.dimensions_load() for more information on formatting.
pixel_sizefloat: The pixel size of the tomogram/tilt series.
tlt_filestr or array-like: The path to the file containing information on tilts (tlt, mdoc, xml) or tilt angles specified as array-like variable. See cryocat.ioutils.tlt_load() for more information on formatting.
z_shiftstr or array-like or int or float, default=0.0: The path to the file containing information on z-shift (txt, com) or z-shift specified as array-like, pandas DataFrame, int or float. See cryocat.ioutils.z_shift_load() for more information on formatting.
ctf_filestr or pandas.DataFrame or array-like, optional: Either the path to the file with defocus values - either in gctf (star), ctffind4 (txt) or warp (xml) format or array like structure of size Nx5 (N is number of tilts), or pandas.DataFrame. See cryocat.ioutils.defocus_load() for more information on formatting.
ctf_file_typestr, {“gctf”, “ctffind4”, “warp”}: The type of the CTF file with defocus values. It can be either “gctf”, “ctffind4”, “warp”, defaults to “gctf”.
dose_filestr or array-like, optional: The path to the file containing information on corrected dose (csv, mdoc, txt, xml) or the corrected dose specified as array-like variable. See cryocat.ioutils.total_dose_load() for more information on formatting.
voltagefloat, default=300.0: The voltage of the microscope, defaults to 300.0.
amp_contrastfloat, default=0.07: The amplitude contrast of the microscope, defaults to 0.07.
csfloat, default=2.7: The spherical aberration coefficient, defaults to 2.7.
output_filestr, optional: The path to the output file, by default None. If None, the output is not written out.
drop_nan_columnsbool, default=True: Whether to drop columns with NaN values, defaults to True.

Returns:

pandas.DataFrame: The wedge list dataframe in STOPGAP format for single tomogram/tilt series.