hyperspy.tests.io package

Submodules

hyperspy.tests.io.generate_dm_testing_files module

Creates Digital Micrograph scripts to generate the dm3 testing files

hyperspy.tests.io.generate_dm_testing_files.generate_1D_files(f, data_types, dmversion)
hyperspy.tests.io.generate_dm_testing_files.generate_2D_files(f, data_types, dmversion)
hyperspy.tests.io.generate_dm_testing_files.generate_3D_files(f, data_types, dmversion)
hyperspy.tests.io.generate_dm_testing_files.generate_4D_files(f, data_types, dmversion)

hyperspy.tests.io.test_bcf module

hyperspy.tests.io.test_bcf.test_decimal_regex()
hyperspy.tests.io.test_bcf.test_fast_bcf()
hyperspy.tests.io.test_bcf.test_get_mode()
hyperspy.tests.io.test_bcf.test_hyperspy_wrap()
hyperspy.tests.io.test_bcf.test_hyperspy_wrap_downsampled()
hyperspy.tests.io.test_bcf.test_load_16bit()
hyperspy.tests.io.test_bcf.test_load_16bit_reduced()
hyperspy.tests.io.test_bcf.test_load_8bit()
hyperspy.tests.io.test_bcf.test_wrong_file()

hyperspy.tests.io.test_blockfile module

hyperspy.tests.io.test_blockfile.save_path()
hyperspy.tests.io.test_blockfile.test_crop_notes(save_path)
hyperspy.tests.io.test_blockfile.test_default_header()
hyperspy.tests.io.test_blockfile.test_different_x_y_scale_units(save_path)
hyperspy.tests.io.test_blockfile.test_load1()
hyperspy.tests.io.test_blockfile.test_load2()
hyperspy.tests.io.test_blockfile.test_load_inplace()
hyperspy.tests.io.test_blockfile.test_load_lazy()
hyperspy.tests.io.test_blockfile.test_load_readonly()
hyperspy.tests.io.test_blockfile.test_load_to_memory()
hyperspy.tests.io.test_blockfile.test_non_square(save_path)
hyperspy.tests.io.test_blockfile.test_save_load_cycle(save_path)
hyperspy.tests.io.test_blockfile.test_write_cutoff(save_path)
hyperspy.tests.io.test_blockfile.test_write_data_am_mismatch(save_path)
hyperspy.tests.io.test_blockfile.test_write_data_line(save_path)
hyperspy.tests.io.test_blockfile.test_write_data_single(save_path)
hyperspy.tests.io.test_blockfile.test_write_fresh(save_path)

hyperspy.tests.io.test_dens module

hyperspy.tests.io.test_dens.test_read1()
hyperspy.tests.io.test_dens.test_read2()
hyperspy.tests.io.test_dens.test_read3()

hyperspy.tests.io.test_dm3 module

class hyperspy.tests.io.test_dm3.TestImageObject

Bases: object

setup_method(method)
test_get_date()
test_get_microscope_name()
test_get_time()
test_parse_string()
hyperspy.tests.io.test_dm3.generate_parameters()
hyperspy.tests.io.test_dm3.test_data(pdict)
hyperspy.tests.io.test_dm3.test_location()
hyperspy.tests.io.test_dm3.test_missing_tag()
hyperspy.tests.io.test_dm3.test_read_Diffraction_metadata()
hyperspy.tests.io.test_dm3.test_read_EDS_metadata()
hyperspy.tests.io.test_dm3.test_read_EELS_metadata()
hyperspy.tests.io.test_dm3.test_read_STEM_metadata()
hyperspy.tests.io.test_dm3.test_read_TEM_metadata()

hyperspy.tests.io.test_dm_stackbuilder_plugin module

class hyperspy.tests.io.test_dm_stackbuilder_plugin.TestStackBuilder

Bases: object

test_load_stackbuilder_imagestack()

hyperspy.tests.io.test_edax module

class hyperspy.tests.io.test_edax.TestSpcSpectrum_v061_xrf

Bases: object

classmethod setup_class()
classmethod teardown_class()
test_axes()
test_data()
test_load_all_spc()
test_parameters()
class hyperspy.tests.io.test_edax.TestSpcSpectrum_v070_eds

Bases: object

classmethod setup_class()
classmethod teardown_class()
test_axes()
test_data()
test_load_all_spc()
test_parameters()
class hyperspy.tests.io.test_edax.TestSpdMap_061_xrf

Bases: object

classmethod setup_class()
classmethod teardown_class()
test_axes()
test_data()
test_ipr_reading()
test_parameters()
test_spc_reading()
class hyperspy.tests.io.test_edax.TestSpdMap_070_eds

Bases: object

classmethod setup_class()
classmethod teardown_class()
test_axes()
test_data()
test_ipr_reading()
test_parameters()
test_spc_reading()
hyperspy.tests.io.test_edax.setup_module()
hyperspy.tests.io.test_edax.teardown_module()

hyperspy.tests.io.test_emd module

class hyperspy.tests.io.test_emd.TestCaseSaveAndRead

Bases: object

teardown_method(method)
test_save_and_read()
class hyperspy.tests.io.test_emd.TestMinimalSave

Bases: object

setup_method(method)
test_minimal_save()
hyperspy.tests.io.test_emd.test_data_axis_length_1()
hyperspy.tests.io.test_emd.test_data_numpy_object_dtype()
hyperspy.tests.io.test_emd.test_image_2d_loading()
hyperspy.tests.io.test_emd.test_metadata()
hyperspy.tests.io.test_emd.test_metadata_with_bytes_string()
hyperspy.tests.io.test_emd.test_signal_3d_loading()
hyperspy.tests.io.test_emd.test_spectrum_1d_loading()

hyperspy.tests.io.test_fei module

class hyperspy.tests.io.test_fei.TestFEIReader

Bases: object

setup_method(method)
test_date_time()
test_guess_units_from_mode()
test_load_acquire()
test_load_diffraction_area_scan()
test_load_diffraction_line_scan()
test_load_diffraction_point()
test_load_emi_old_new_format()
test_load_image_content()
test_load_multisignal_stack()
test_load_multisignal_stack_mismatch()
test_load_ser_reader_old_new_format()
test_load_spectrum_area_scan()
test_load_spectrum_area_scan_not_square()
test_load_spectrum_line_scan()
test_load_spectrum_point()
test_load_stack_image_preview()
test_load_units_scale()
test_metadata_STEM()
test_metadata_TEM()
test_metadata_diffraction()
test_read_STEM_TEM_mode()

hyperspy.tests.io.test_hdf5 module

class hyperspy.tests.io.test_hdf5.Example1

Bases: object

test_data()
test_original_metadata()
class hyperspy.tests.io.test_hdf5.TestAxesConfiguration

Bases: object

setup_method(method)
teardown_method(method)
test_axes_configuration()
class hyperspy.tests.io.test_hdf5.TestExample1_10

Bases: hyperspy.tests.io.test_hdf5.Example1

setup_method(method)
class hyperspy.tests.io.test_hdf5.TestExample1_11

Bases: hyperspy.tests.io.test_hdf5.Example1

setup_method(method)
class hyperspy.tests.io.test_hdf5.TestExample1_12

Bases: hyperspy.tests.io.test_hdf5.Example1

setup_method(method)
test_date()
test_time()
class hyperspy.tests.io.test_hdf5.TestLoadingNewSavedMetadata

Bases: object

setup_method(method)
test_binary_string()
test_empty_things()
test_inside_things()
test_signal_inside()
test_simple_things()
class hyperspy.tests.io.test_hdf5.TestLoadingOOMReadOnly

Bases: object

setup_method(method)
teardown_method(method)
test_oom_loading()
class hyperspy.tests.io.test_hdf5.TestPassingArgs

Bases: object

setup_method(method)
teardown_method(method)
test_compression_opts()
class hyperspy.tests.io.test_hdf5.TestSavingMetadataContainers

Bases: object

setup_method(method)
test_date_time(tmpfilepath)
test_general_metadata(tmpfilepath)
test_general_type_not_working(tmpfilepath)
test_metadata_update_to_v3_0()
test_numpy_general_type(tmpfilepath)
test_numpy_only_inner_lists(tmpfilepath)
test_quantity(tmpfilepath)
test_save_long_list(tmpfilepath)
test_save_unicode(tmpfilepath)
test_unsupported_type(tmpfilepath)
class hyperspy.tests.io.test_hdf5.Test_permanent_markers_io

Bases: object

test_load_missing_y2_value()
test_load_unknown_marker_type()
test_save_load_empty_metadata_markers(mpl_cleanup)
test_save_load_horizontal_line_marker(mpl_cleanup)
test_save_load_horizontal_line_segment_marker(mpl_cleanup)
test_save_load_line_segment_marker(mpl_cleanup)
test_save_load_multidim_navigation_marker(mpl_cleanup)
test_save_load_permanent_marker(mpl_cleanup)
test_save_load_permanent_marker_all_types(mpl_cleanup)
test_save_load_point_marker(mpl_cleanup)
test_save_load_rectangle_marker(mpl_cleanup)
test_save_load_text_marker(mpl_cleanup)
test_save_load_vertical_line_marker(mpl_cleanup)
test_save_load_vertical_line_segment_marker(mpl_cleanup)
test_save_permanent_marker(mpl_cleanup)
hyperspy.tests.io.test_hdf5.test_lazy_metadata_arrays(tmpfilepath)
hyperspy.tests.io.test_hdf5.test_none_metadata()
hyperspy.tests.io.test_hdf5.test_rgba16()
hyperspy.tests.io.test_hdf5.test_strings_from_py2()
hyperspy.tests.io.test_hdf5.tmpfilepath()

hyperspy.tests.io.test_io module

class hyperspy.tests.io.test_io.TestIOOverwriting

Bases: object

setup_method(method)
teardown_method(method)
test_io_overwriting_False()
test_io_overwriting_None_existing_file_n()
test_io_overwriting_None_existing_file_y()
test_io_overwriting_True()
test_io_overwriting_no_existing_file(overwrite)

hyperspy.tests.io.test_msa module

class hyperspy.tests.io.test_msa.TestExample1

Bases: object

setup_method(method)
test_data()
test_metadata()
test_parameters()
test_write_load_cycle()
class hyperspy.tests.io.test_msa.TestExample2

Bases: object

setup_method(method)
test_data()
test_metadata()
test_parameters()
test_write_load_cycle()
hyperspy.tests.io.test_msa.test_minimum_metadata_example()

hyperspy.tests.io.test_protochips module

class hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader

Bases: object

setup_method(method)
test_read_column_name()
test_read_data()
test_read_start_datetime()
class hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader

Bases: object

setup_method(method)
test_read_column_name()
test_read_data()
test_read_start_datetime()
class hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSV

Bases: object

setup_method(method)
test_read_metadata()
test_read_original_metadata()
class hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVNoUser

Bases: object

setup_method(method)
test_read_metadata()
test_read_original_metadata()
class hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader

Bases: object

setup_method(method)
test_read_column_name()
test_read_data()
test_read_metadata_header()
test_read_start_datetime()
class hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader

Bases: object

setup_method(method)
test_read_column_name()
test_read_data()
test_read_start_datetime()
hyperspy.tests.io.test_protochips.create_numpy_file(filename, obj)
hyperspy.tests.io.test_protochips.get_datetime(dt)
hyperspy.tests.io.test_protochips.test_loading_invalid_protochips_file()
hyperspy.tests.io.test_protochips.test_loading_random_csv_file()
hyperspy.tests.io.test_protochips.test_read_protochips_electrical()
hyperspy.tests.io.test_protochips.test_read_protochips_electrothermal()
hyperspy.tests.io.test_protochips.test_read_protochips_gas_cell()
hyperspy.tests.io.test_protochips.test_read_protochips_thermal()

hyperspy.tests.io.test_ripple module

hyperspy.tests.io.test_ripple.generate_files()

Generate the test files that are distributed with HyperSpy.

Unless new features are introduced there shouldn’t be any need to recreate the files.

hyperspy.tests.io.test_ripple.generate_parameters()
hyperspy.tests.io.test_ripple.test_data(pdict)
hyperspy.tests.io.test_ripple.test_write_unsupported_data_shape()
hyperspy.tests.io.test_ripple.test_write_unsupported_data_type()
hyperspy.tests.io.test_ripple.test_write_with_metadata()
hyperspy.tests.io.test_ripple.test_write_without_metadata()

hyperspy.tests.io.test_semper_unf module

class hyperspy.tests.io.test_semper_unf.TestCaseSaveAndReadByte

Bases: object

teardown_method(method)
test_save_and_read()
class hyperspy.tests.io.test_semper_unf.TestCaseSaveAndReadImage

Bases: object

teardown_method(method)
test_save_and_read()
hyperspy.tests.io.test_semper_unf.test_image_2d_loading()
hyperspy.tests.io.test_semper_unf.test_image_byte_loading()
hyperspy.tests.io.test_semper_unf.test_image_complex_loading()
hyperspy.tests.io.test_semper_unf.test_image_int16_loading()
hyperspy.tests.io.test_semper_unf.test_image_int32_loading()
hyperspy.tests.io.test_semper_unf.test_no_label_loading()
hyperspy.tests.io.test_semper_unf.test_signal_3d_loading()
hyperspy.tests.io.test_semper_unf.test_spectrum_1d_loading()
hyperspy.tests.io.test_semper_unf.test_with_title_loading()
hyperspy.tests.io.test_semper_unf.test_writing_loading_metadata()
hyperspy.tests.io.test_semper_unf.test_writing_unsupported_data_type()

hyperspy.tests.io.test_tiff module

hyperspy.tests.io.test_tiff.test_read_BW_Zeiss_optical_scale_metadata()
hyperspy.tests.io.test_tiff.test_read_BW_Zeiss_optical_scale_metadata2()
hyperspy.tests.io.test_tiff.test_read_BW_Zeiss_optical_scale_metadata3()
hyperspy.tests.io.test_tiff.test_read_FEI_SEM_scale_metadata_16bits()
hyperspy.tests.io.test_tiff.test_read_FEI_SEM_scale_metadata_8bits()
hyperspy.tests.io.test_tiff.test_read_RGB_Zeiss_optical_scale_metadata()
hyperspy.tests.io.test_tiff.test_read_TVIPS_metadata()
hyperspy.tests.io.test_tiff.test_read_Zeiss_SEM_scale_metadata_1k_image()
hyperspy.tests.io.test_tiff.test_read_unit_from_DM_stack()
hyperspy.tests.io.test_tiff.test_read_unit_from_imagej()
hyperspy.tests.io.test_tiff.test_read_unit_from_imagej_no_scale()
hyperspy.tests.io.test_tiff.test_read_unit_from_imagej_stack()
hyperspy.tests.io.test_tiff.test_read_unit_from_imagej_stack_no_scale()
hyperspy.tests.io.test_tiff.test_read_unit_um()
hyperspy.tests.io.test_tiff.test_rgba16()
hyperspy.tests.io.test_tiff.test_saving_loading_stack_no_scale()
hyperspy.tests.io.test_tiff.test_saving_with_custom_tag()
hyperspy.tests.io.test_tiff.test_write_read_intensity_axes_DM()
hyperspy.tests.io.test_tiff.test_write_read_unit_imagej()
hyperspy.tests.io.test_tiff.test_write_read_unit_imagej_with_description()
hyperspy.tests.io.test_tiff.test_write_scale_unit()
hyperspy.tests.io.test_tiff.test_write_scale_unit_image_stack()

Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct

hyperspy.tests.io.test_tiff.test_write_scale_unit_no_export_scale()
hyperspy.tests.io.test_tiff.test_write_scale_unit_not_square_pixel()

Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct

hyperspy.tests.io.test_tiff.test_write_scale_with_um_unit()

Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct

hyperspy.tests.io.test_tiff.test_write_scale_with_undefined_scale()

Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct

hyperspy.tests.io.test_tiff.test_write_scale_with_undefined_unit()

Lazy test, still need to open the files in ImageJ or DM to check if the scale and unit are correct

Module contents