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

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

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)

Bases: sas.sascalc.dataloader.data_info.plottable_1D, sas.sascalc.dataloader.data_info.DataInfo

1D data class

clone_without_data(length=0, clone=None)

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)

copy values of Data1D of type DataLaoder.Data_info

is_slit_smeared()

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)

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)

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)

copy value of Data2D of type DataLoader.data_info

isSesans = False

class sas.sascalc.dataloader.data_info.DataInfo

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='')

Add notes to datainfo

append_empty_process()

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

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

Bases: object

Class that holds information about the processes performed on the data.

date = ''

description = ''

is_empty()

Return True if the object is empty

name = ''

notes = None

single_line_desc()

Return a single line string representing the process

term = None

class sas.sascalc.dataloader.data_info.Sample

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

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

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)

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)

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)

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)

set the x axis label and unit

y = None

yaxis(label, unit)

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)

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)

set the x axis label and unit

xmax = None

xmin = None

y_bins = None

yaxis(label, unit)

set the y axis label and unit

ymax = None

ymin = None

zaxis(label, unit)

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

Bases: object

allow_all = False

convert_data_units(default_q_unit='1/A')

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()

Clean up the data sets and refresh everything :return: None

deprecated_extensions = ['.asc']

ext = ['.txt']

format_unit(unit=None)

Format units a common way :param unit: :return:

get_file_contents()

Reader specific class to access the contents of the file All reader classes that inherit from FileReader must implement

handle_error_message(msg)

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()

Returns the next line in the file as a string.

nextlines()

Returns the next line in the file as a string.

read(filepath)

Basic file reader

Parameters:filepath – The full or relative path to a file to be loaded

readall()

Returns the entire file as a string.

remove_empty_q_values()

Remove any point where Q == 0

reset_data_list(no_lines=0)

Reset the plottable_1D object

reset_state()

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()

Helper that automatically combines the info and set and then appends it to output

set_all_to_none()

Set all mutable values to None for error handling purposes

static set_default_1d_units(data)

Set the x and y axes to the default 1D units :param data: 1D data set :return:

static set_default_2d_units(data)

Set the x and y axes to the default 2D units :param data: 2D data set :return:

sort_data()

Sort 1D data along the X axis for consistency

static splitline(line)

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)

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

Bases: object

Utility class to use the Registry as a singleton.

associate_file_reader(ext, loader)

Append a reader object to readers :param ext: file extension [string] :param module: reader object

associate_file_type(ext, module)

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)

Find plugins in a given directory :param dir: directory to look into to find new readers/writers

get_wildcards()

Return the list of wildcards

load(file, format=None)

Load a file :param file: file name (path) :param format: specified format to use (optional) :return: DataInfo object

save(file, data, format)

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

Bases: sas.sascalc.data_util.registry.ExtensionRegistry

Registry class for file format extensions. Readers and writers are supported.

associate_file_reader(ext, loader)

Append a reader object to readers :param ext: file extension [string] :param module: reader object

associate_file_type(ext, module)

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)

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)

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)

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)

Returns:the loader associated with the file type of path. Raises ValueError:  if file type is not known.

save(path, data, format=None)

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)

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)

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)

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)

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)

Bases: object

This class just creates a binning object either linear or log

get_bin_index(value)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Bases: sas.sascalc.dataloader.manipulations._Slab

Compute average I(Qy) for a region of interest

sas.sascalc.dataloader.manipulations.flip_phi(phi)

Correct phi to within the 0 <= to <= 2pi range

Returns:phi in >=0 and <=2Pi

sas.sascalc.dataloader.manipulations.get_dq_data(data2D)

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)

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)

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)

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)

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)

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)

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

Module contents