sas.sascalc.dataloader package
Subpackages
- sas.sascalc.dataloader.readers package
- Submodules
- sas.sascalc.dataloader.readers.abs_reader module
- sas.sascalc.dataloader.readers.anton_paar_saxs_reader module
- sas.sascalc.dataloader.readers.ascii_reader module
- sas.sascalc.dataloader.readers.associations module
- sas.sascalc.dataloader.readers.cansas_constants module
- sas.sascalc.dataloader.readers.cansas_reader module
- sas.sascalc.dataloader.readers.cansas_reader_HDF5 module
- sas.sascalc.dataloader.readers.danse_reader module
- sas.sascalc.dataloader.readers.red2d_reader module
- sas.sascalc.dataloader.readers.sesans_reader module
- sas.sascalc.dataloader.readers.tiff_reader module
- sas.sascalc.dataloader.readers.xml_reader module
- Module contents
Submodules
sas.sascalc.dataloader.data_info module
Module that contains classes to hold information read from reduced data files.
A good description of the data members can be found in the CanSAS 1D XML data format:
http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation
- class sas.sascalc.dataloader.data_info.Aperture[source]
Bases:
object
- distance = None
- distance_unit = 'mm'
- name = None
- size = None
- size_name = None
- size_unit = 'mm'
- type = None
- class sas.sascalc.dataloader.data_info.Collimation[source]
Bases:
object
Class to hold collimation information
- aperture = None
- length = None
- length_unit = 'mm'
- name = None
- class sas.sascalc.dataloader.data_info.Data1D(x=None, y=None, dx=None, dy=None, lam=None, dlam=None, isSesans=False)[source]
Bases:
sas.sascalc.dataloader.data_info.plottable_1D
,sas.sascalc.dataloader.data_info.DataInfo
1D data class
- clone_without_data(length=0, clone=None)[source]
Clone the current object, without copying the data (which will be filled out by a subsequent operation). The data arrays will be initialized to zero.
- Parameters
length – length of the data array to be initialized
clone – if provided, the data will be copied to clone
- copy_from_datainfo(data1d)[source]
copy values of Data1D of type DataLaoder.Data_info
- is_slit_smeared()[source]
Check whether the data has slit smearing information :return: True is slit smearing info is present, False otherwise
- class sas.sascalc.dataloader.data_info.Data2D(data=None, err_data=None, qx_data=None, qy_data=None, q_data=None, mask=None, dqx_data=None, dqy_data=None, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None)[source]
Bases:
sas.sascalc.dataloader.data_info.plottable_2D
,sas.sascalc.dataloader.data_info.DataInfo
2D data class
- I_unit = '1/cm'
- Q_unit = '1/A'
- clone_without_data(length=0, clone=None)[source]
Clone the current object, without copying the data (which will be filled out by a subsequent operation). The data arrays will be initialized to zero.
- Parameters
length – length of the data array to be initialized
clone – if provided, the data will be copied to clone
- copy_from_datainfo(data2d)[source]
copy value of Data2D of type DataLoader.data_info
- isSesans = False
- class sas.sascalc.dataloader.data_info.DataInfo[source]
Bases:
object
Class to hold the data read from a file. It includes four blocks of data for the instrument description, the sample description, the data itself and any other meta data.
- add_notes(message='')[source]
Add notes to datainfo
- append_empty_process()[source]
- collimation = None
- detector = None
- errors = None
- filename = ''
- instrument = ''
- isSesans = None
- meta_data = None
- notes = None
- process = None
- run = None
- run_name = None
- sample = None
- source = None
- title = ''
- trans_spectrum = None
- class sas.sascalc.dataloader.data_info.Detector[source]
Bases:
object
Class to hold detector information
- beam_center = None
- beam_center_unit = 'mm'
- distance = None
- distance_unit = 'mm'
- name = None
- offset = None
- offset_unit = 'm'
- orientation = None
- orientation_unit = 'degree'
- pixel_size = None
- pixel_size_unit = 'mm'
- slit_length = None
- slit_length_unit = 'mm'
- class sas.sascalc.dataloader.data_info.Process[source]
Bases:
object
Class that holds information about the processes performed on the data.
- date = ''
- description = ''
- is_empty()[source]
Return True if the object is empty
- name = ''
- notes = None
- single_line_desc()[source]
Return a single line string representing the process
- term = None
- class sas.sascalc.dataloader.data_info.Sample[source]
Bases:
object
Class to hold the sample description
- ID = ''
- details = None
- name = ''
- orientation = None
- orientation_unit = 'degree'
- position = None
- position_unit = 'mm'
- temperature = None
- temperature_unit = None
- thickness = None
- thickness_unit = 'mm'
- transmission = None
- yacceptance = (0, '')
- zacceptance = (0, '')
- class sas.sascalc.dataloader.data_info.Source[source]
Bases:
object
Class to hold source information
- beam_shape = None
- beam_size = None
- beam_size_name = None
- beam_size_unit = 'mm'
- name = None
- probe = None
- radiation = None
- type = None
- wavelength = None
- wavelength_max = None
- wavelength_max_unit = 'nm'
- wavelength_min = None
- wavelength_min_unit = 'nm'
- wavelength_spread = None
- wavelength_spread_unit = 'percent'
- wavelength_unit = 'A'
- class sas.sascalc.dataloader.data_info.TransmissionSpectrum[source]
Bases:
object
Class that holds information about transmission spectrum for white beams and spallation sources.
- name = ''
- timestamp = ''
- transmission = None
- transmission_deviation = None
- transmission_deviation_unit = ''
- transmission_unit = ''
- wavelength = None
- wavelength_unit = 'A'
- class sas.sascalc.dataloader.data_info.Vector(x=None, y=None, z=None)[source]
Bases:
object
Vector class to hold multi-dimensional objects
- x = None
- y = None
- z = None
- sas.sascalc.dataloader.data_info.combine_data_info_with_plottable(data, datainfo)[source]
A function that combines the DataInfo data in self.current_datainto with a plottable_1D or 2D data object.
- Parameters
data – A plottable_1D or plottable_2D data object
datainfo – A DataInfo object to be combined with the plottable
- Returns
A fully specified Data1D or Data2D object
- class sas.sascalc.dataloader.data_info.plottable_1D(x, y, dx=None, dy=None, dxl=None, dxw=None, lam=None, dlam=None)[source]
Bases:
object
Data1D is a place holder for 1D plottables.
- dlam = None
- dx = None
- dxl = None
- dxw = None
- dy = None
- lam = None
- x = None
- xaxis(label, unit)[source]
set the x axis label and unit
- y = None
- yaxis(label, unit)[source]
set the y axis label and unit
- class sas.sascalc.dataloader.data_info.plottable_2D(data=None, err_data=None, qx_data=None, qy_data=None, q_data=None, mask=None, dqx_data=None, dqy_data=None, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None, x_bins=None, y_bins=None)[source]
Bases:
object
Data2D is a place holder for 2D plottables.
- data = None
- dqx_data = None
- dqy_data = None
- err_data = None
- mask = None
- q_data = None
- qx_data = None
- qy_data = None
- x_bins = None
- xaxis(label, unit)[source]
set the x axis label and unit
- xmax = None
- xmin = None
- y_bins = None
- yaxis(label, unit)[source]
set the y axis label and unit
- ymax = None
- ymin = None
- zaxis(label, unit)[source]
set the z axis label and unit
sas.sascalc.dataloader.file_reader_base_class module
This is the base file reader class most file readers should inherit from. All generic functionality required for a file loader/reader is built into this class
- class sas.sascalc.dataloader.file_reader_base_class.FileReader[source]
Bases:
object
- allow_all = False
- convert_data_units(default_q_unit='1/A')[source]
Converts al; data to the sasview default of units of A^{-1} for Q and cm^{-1} for I. :param default_q_unit: The default Q unit used by Sasview
- data_cleanup()[source]
Clean up the data sets and refresh everything :return: None
- deprecated_extensions = ['.asc']
- ext = ['.txt']
- format_unit(unit=None)[source]
Format units a common way :param unit: :return:
- abstract get_file_contents()[source]
Reader specific class to access the contents of the file All reader classes that inherit from FileReader must implement
- handle_error_message(msg)[source]
Generic error handler to add an error to the current datainfo to propagate the error up the error chain. :param msg: Error message
- has_converter = True
- nextline()[source]
Returns the next line in the file as a string.
- nextlines()[source]
Returns the next line in the file as a string.
- read(filepath)[source]
Basic file reader
- Parameters
filepath – The full or relative path to a file to be loaded
- readall()[source]
Returns the entire file as a string.
- remove_empty_q_values()[source]
Remove any point where Q == 0
- reset_data_list(no_lines=0)[source]
Reset the plottable_1D object
- reset_state()[source]
Resets the class state to a base case when loading a new data file so previous data files do not appear a second time
- send_to_output()[source]
Helper that automatically combines the info and set and then appends it to output
- set_all_to_none()[source]
Set all mutable values to None for error handling purposes
- static set_default_1d_units(data)[source]
Set the x and y axes to the default 1D units :param data: 1D data set :return:
- static set_default_2d_units(data)[source]
Set the x and y axes to the default 2D units :param data: 2D data set :return:
- sort_data()[source]
Sort 1D data along the X axis for consistency
- static splitline(line)[source]
Splits a line into pieces based on common delimiters :param line: A single line of text :return: list of values
- type = ['Text files (*.txt|*.TXT)']
- type_name = 'ASCII'
- sas.sascalc.dataloader.file_reader_base_class.decode(s)[source]
sas.sascalc.dataloader.loader module
File handler to support different file extensions. Uses reflectometer registry utility. The default readers are found in the ‘readers’ sub-module and registered by default at initialization time. To add a new default reader, one must register it in the register_readers method found in readers/__init__.py. A utility method (find_plugins) is available to inspect a directory (for instance, a user plug-in directory) and look for new readers/writers.
- class sas.sascalc.dataloader.loader.Loader[source]
Bases:
object
Utility class to use the Registry as a singleton.
- associate_file_reader(ext, loader)[source]
Append a reader object to readers :param ext: file extension [string] :param module: reader object
- associate_file_type(ext, module)[source]
Look into a module to find whether it contains a Reader class. If so, append it to readers and (potentially) to the list of writers for the given extension :param ext: file extension [string] :param module: module object
- find_plugins(directory)[source]
Find plugins in a given directory :param dir: directory to look into to find new readers/writers
- get_wildcards()[source]
Return the list of wildcards
- load(file, format=None)[source]
Load a file :param file: file name (path) :param format: specified format to use (optional) :return: DataInfo object
- save(file, data, format)[source]
Save a DataInfo object to file :param file: file name (path) :param data: DataInfo object :param format: format to write the data in
- class sas.sascalc.dataloader.loader.Registry[source]
Bases:
sas.sascalc.data_util.registry.ExtensionRegistry
Registry class for file format extensions. Readers and writers are supported.
- associate_file_reader(ext, loader)[source]
Append a reader object to readers :param ext: file extension [string] :param module: reader object
- associate_file_type(ext, module)[source]
Look into a module to find whether it contains a Reader class. If so, APPEND it to readers and (potentially) to the list of writers for the given extension :param ext: file extension [string] :param module: module object
- find_plugins(dir)[source]
Find readers in a given directory. This method can be used to inspect user plug-in directories to find new readers/writers. :param dir: directory to search into :return: number of readers found
- load(path, format=None, debug=False, use_defaults=True)[source]
Call the loader for the file type of path.
- Parameters
path – file path
format – explicit extension, to force the use of a particular reader
debug – when True, print the traceback for each loader that fails
use_defaults – Flag to use the default readers as a backup if the main reader fails or no reader exists
Defaults to the ascii (multi-column), cansas XML, and cansas NeXuS readers if no reader was registered for the file’s extension.
- load_using_generic_loaders(path)[source]
If the expected reader cannot load the file or no known loader exists, attempt to load the file using a few defaults readers :param path: file path :return: List of Data1D and Data2D objects
- lookup_writers(path)[source]
- Returns
the loader associated with the file type of path.
- Raises ValueError
if file type is not known.
- save(path, data, format=None)[source]
Call the writer for the file type of path. Raises ValueError if no writer is available. Raises KeyError if format is not available. May raise a writer-defined exception if writer fails.
sas.sascalc.dataloader.loader_exceptions module
Exceptions specific to loading data.
- exception sas.sascalc.dataloader.loader_exceptions.DataReaderException(e=None)[source]
Bases:
Exception
Exception for files that were able to mostly load, but had minor issues along the way. Any exceptions of this type should be put into the datainfo.errors
- exception sas.sascalc.dataloader.loader_exceptions.DefaultReaderException(e=None)[source]
Bases:
Exception
Exception for files with no associated reader. This should be thrown by default readers only to tell Loader to try the next reader.
- exception sas.sascalc.dataloader.loader_exceptions.FileContentsException(e=None)[source]
Bases:
Exception
Exception for files with an associated reader, but with no loadable data. This is useful for catching loader or file format issues.
- exception sas.sascalc.dataloader.loader_exceptions.NoKnownLoaderException(e=None)[source]
Bases:
Exception
Exception for files with no associated reader based on the file extension of the loaded file. This exception should only be thrown by loader.py.
sas.sascalc.dataloader.manipulations module
- class sas.sascalc.dataloader.manipulations.Binning(min_value, max_value, n_bins, base=None)[source]
Bases:
object
This class just creates a binning object either linear or log
- get_bin_index(value)[source]
The general formula logarithm binning is: bin = floor(N * (log(x) - log(min)) / (log(max) - log(min)))
- class sas.sascalc.dataloader.manipulations.Boxavg(x_min=0.0, x_max=0.0, y_min=0.0, y_max=0.0)[source]
Bases:
sas.sascalc.dataloader.manipulations.Boxsum
Perform the average of counts in a 2D region of interest.
- class sas.sascalc.dataloader.manipulations.Boxcut(x_min=0.0, x_max=0.0, y_min=0.0, y_max=0.0)[source]
Bases:
object
Find a rectangular 2D region of interest.
- class sas.sascalc.dataloader.manipulations.Boxsum(x_min=0.0, x_max=0.0, y_min=0.0, y_max=0.0)[source]
Bases:
object
Perform the sum of counts in a 2D region of interest.
- class sas.sascalc.dataloader.manipulations.CircularAverage(r_min=0.0, r_max=0.0, bin_width=0.0005)[source]
Bases:
object
Perform circular averaging on 2D data
The data returned is the distribution of counts as a function of Q
- class sas.sascalc.dataloader.manipulations.Ring(r_min=0, r_max=0, center_x=0, center_y=0, nbins=36)[source]
Bases:
object
Defines a ring on a 2D data set. The ring is defined by r_min, r_max, and the position of the center of the ring.
The data returned is the distribution of counts around the ring as a function of phi.
Phi_min and phi_max should be defined between 0 and 2*pi in anti-clockwise starting from the x- axis on the left-hand side
- class sas.sascalc.dataloader.manipulations.Ringcut(r_min=0, r_max=0, center_x=0, center_y=0)[source]
Bases:
object
Defines a ring on a 2D data set. The ring is defined by r_min, r_max, and the position of the center of the ring.
The data returned is the region inside the ring
Phi_min and phi_max should be defined between 0 and 2*pi in anti-clockwise starting from the x- axis on the left-hand side
- class sas.sascalc.dataloader.manipulations.SectorPhi(r_min, r_max, phi_min=0, phi_max=6.283185307179586, nbins=20, base=None)[source]
Bases:
sas.sascalc.dataloader.manipulations._Sector
Sector average as a function of phi. I(phi) is return and the data is averaged over Q.
A sector is defined by r_min, r_max, phi_min, phi_max. The number of bin in phi also has to be defined.
- class sas.sascalc.dataloader.manipulations.SectorQ(r_min, r_max, phi_min=0, phi_max=6.283185307179586, nbins=20, base=None)[source]
Bases:
sas.sascalc.dataloader.manipulations._Sector
Sector average as a function of Q for both symatric wings. I(Q) is return and the data is averaged over phi.
A sector is defined by r_min, r_max, phi_min, phi_max. r_min, r_max, phi_min, phi_max >0. The number of bin in Q also has to be defined.
- class sas.sascalc.dataloader.manipulations.Sectorcut(phi_min=0, phi_max=3.141592653589793)[source]
Bases:
object
Defines a sector (major + minor) region on a 2D data set. The sector is defined by phi_min, phi_max, where phi_min and phi_max are defined by the right and left lines wrt central line.
Phi_min and phi_max are given in units of radian and (phi_max-phi_min) should not be larger than pi
- class sas.sascalc.dataloader.manipulations.SlabX(x_min=0.0, x_max=0.0, y_min=0.0, y_max=0.0, bin_width=0.001, fold=False)[source]
Bases:
sas.sascalc.dataloader.manipulations._Slab
Compute average I(Qx) for a region of interest
- class sas.sascalc.dataloader.manipulations.SlabY(x_min=0.0, x_max=0.0, y_min=0.0, y_max=0.0, bin_width=0.001, fold=False)[source]
Bases:
sas.sascalc.dataloader.manipulations._Slab
Compute average I(Qy) for a region of interest
- sas.sascalc.dataloader.manipulations.flip_phi(phi)[source]
Correct phi to within the 0 <= to <= 2pi range
- Returns
phi in >=0 and <=2Pi
- sas.sascalc.dataloader.manipulations.get_dq_data(data2D)[source]
Get the dq for resolution averaging The pinholes and det. pix contribution present in both direction of the 2D which must be subtracted when converting to 1D: dq_overlap should calculated ideally at q = 0. Note This method works on only pinhole geometry. Extrapolate dqx(r) and dqy(phi) at q = 0, and take an average.
- sas.sascalc.dataloader.manipulations.get_intercept(q, q_0, q_1)[source]
Returns the fraction of the side at which the q-value intercept the pixel, None otherwise. The values returned is the fraction ON THE SIDE OF THE LOWEST Q.
A B +-----------+--------+ <--- pixel size 0 1 Q_0 -------- Q ----- Q_1 <--- equivalent Q range if Q_1 > Q_0, A is returned if Q_1 < Q_0, B is returned if Q is outside the range of [Q_0, Q_1], None is returned
- sas.sascalc.dataloader.manipulations.get_pixel_fraction(qmax, q_00, q_01, q_10, q_11)[source]
Returns the fraction of the pixel defined by the four corners (q_00, q_01, q_10, q_11) that has q < qmax.:
q_01 q_11 y=1 +--------------+ | | | | | | y=0 +--------------+ q_00 q_10 x=0 x=1
- sas.sascalc.dataloader.manipulations.get_pixel_fraction_square(x, xmin, xmax)[source]
Return the fraction of the length from xmin to x.:
A B +-----------+---------+ xmin x xmax
- Parameters
x – x-value
xmin – minimum x for the length considered
xmax – minimum x for the length considered
- Returns
(x-xmin)/(xmax-xmin) when xmin < x < xmax
- sas.sascalc.dataloader.manipulations.get_q(dx, dy, det_dist, wavelength)[source]
- Parameters
dx – x-distance from beam center [mm]
dy – y-distance from beam center [mm]
- Returns
q-value at the given position
- sas.sascalc.dataloader.manipulations.get_q_compo(dx, dy, det_dist, wavelength, compo=None)[source]
This reduces tiny error at very large q. Implementation of this func is not started yet.<–ToDo
- sas.sascalc.dataloader.manipulations.reader2D_converter(data2d=None)[source]
convert old 2d format opened by IhorReader or danse_reader to new Data2D format This is mainly used by the Readers
- Parameters
data2d – 2d array of Data2D object
- Returns
1d arrays of Data2D object