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icometrix/dicom2nifti | dicom2nifti/common.py | write_bval_file | def write_bval_file(bvals, bval_file):
"""
Write an array of bvals to a bval file
:param bvals: array with the values
:param bval_file: filepath to write to
"""
if bval_file is None:
return
logger.info('Saving BVAL file: %s' % bval_file)
with open(bval_file, 'w') as text_file:
... | python | def write_bval_file(bvals, bval_file):
"""
Write an array of bvals to a bval file
:param bvals: array with the values
:param bval_file: filepath to write to
"""
if bval_file is None:
return
logger.info('Saving BVAL file: %s' % bval_file)
with open(bval_file, 'w') as text_file:
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icometrix/dicom2nifti | dicom2nifti/common.py | create_affine | def create_affine(sorted_dicoms):
"""
Function to generate the affine matrix for a dicom series
This method was based on (http://nipy.org/nibabel/dicom/dicom_orientation.html)
:param sorted_dicoms: list with sorted dicom files
"""
# Create affine matrix (http://nipy.sourceforge.net/nibabel/dic... | python | def create_affine(sorted_dicoms):
"""
Function to generate the affine matrix for a dicom series
This method was based on (http://nipy.org/nibabel/dicom/dicom_orientation.html)
:param sorted_dicoms: list with sorted dicom files
"""
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icometrix/dicom2nifti | dicom2nifti/common.py | is_orthogonal | def is_orthogonal(dicoms, log_details=False):
"""
Validate that volume is orthonormal
:param dicoms: check that we have a volume without skewing
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6... | python | def is_orthogonal(dicoms, log_details=False):
"""
Validate that volume is orthonormal
:param dicoms: check that we have a volume without skewing
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6... | [
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icometrix/dicom2nifti | dicom2nifti/common.py | is_orthogonal_nifti | def is_orthogonal_nifti(nifti_file):
"""
Validate that volume is orthonormal
:param dicoms: check that we have a volume without skewing
"""
nifti_image = nibabel.load(nifti_file)
affine = nifti_image.affine
transformed_x = numpy.transpose(numpy.dot(affine, [[1], [0], [0], [0]]))[0][:3]
... | python | def is_orthogonal_nifti(nifti_file):
"""
Validate that volume is orthonormal
:param dicoms: check that we have a volume without skewing
"""
nifti_image = nibabel.load(nifti_file)
affine = nifti_image.affine
transformed_x = numpy.transpose(numpy.dot(affine, [[1], [0], [0], [0]]))[0][:3]
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icometrix/dicom2nifti | dicom2nifti/common.py | sort_dicoms | def sort_dicoms(dicoms):
"""
Sort the dicoms based om the image possition patient
:param dicoms: list of dicoms
"""
# find most significant axis to use during sorting
# the original way of sorting (first x than y than z) does not work in certain border situations
# where for exampe the X wi... | python | def sort_dicoms(dicoms):
"""
Sort the dicoms based om the image possition patient
:param dicoms: list of dicoms
"""
# find most significant axis to use during sorting
# the original way of sorting (first x than y than z) does not work in certain border situations
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icometrix/dicom2nifti | dicom2nifti/common.py | validate_slice_increment | def validate_slice_increment(dicoms):
"""
Validate that the distance between all slices is equal (or very close to)
:param dicoms: list of dicoms
"""
first_image_position = numpy.array(dicoms[0].ImagePositionPatient)
previous_image_position = numpy.array(dicoms[1].ImagePositionPatient)
inc... | python | def validate_slice_increment(dicoms):
"""
Validate that the distance between all slices is equal (or very close to)
:param dicoms: list of dicoms
"""
first_image_position = numpy.array(dicoms[0].ImagePositionPatient)
previous_image_position = numpy.array(dicoms[1].ImagePositionPatient)
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icometrix/dicom2nifti | dicom2nifti/common.py | is_slice_increment_inconsistent | def is_slice_increment_inconsistent(dicoms):
"""
Validate that the distance between all slices is equal (or very close to)
:param dicoms: list of dicoms
"""
sliceincrement_inconsistent = False
first_image_position = numpy.array(dicoms[0].ImagePositionPatient)
previous_image_position = numpy... | python | def is_slice_increment_inconsistent(dicoms):
"""
Validate that the distance between all slices is equal (or very close to)
:param dicoms: list of dicoms
"""
sliceincrement_inconsistent = False
first_image_position = numpy.array(dicoms[0].ImagePositionPatient)
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icometrix/dicom2nifti | dicom2nifti/common.py | validate_orientation | def validate_orientation(dicoms):
"""
Validate that all dicoms have the same orientation
:param dicoms: list of dicoms
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6]
for dicom_ in dicoms... | python | def validate_orientation(dicoms):
"""
Validate that all dicoms have the same orientation
:param dicoms: list of dicoms
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6]
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icometrix/dicom2nifti | dicom2nifti/common.py | set_tr_te | def set_tr_te(nifti_image, repetition_time, echo_time):
"""
Set the tr and te in the nifti headers
:param echo_time: echo time
:param repetition_time: repetition time
:param nifti_image: nifti image to set the info to
"""
# set the repetition time in pixdim
nifti_image.header.structarr[... | python | def set_tr_te(nifti_image, repetition_time, echo_time):
"""
Set the tr and te in the nifti headers
:param echo_time: echo time
:param repetition_time: repetition time
:param nifti_image: nifti image to set the info to
"""
# set the repetition time in pixdim
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: the filepath to the output n... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _is_diffusion_imaging | def _is_diffusion_imaging(grouped_dicoms):
"""
Use this function to detect if a dicom series is a ge dti dataset
NOTE: We already assume this is a 4D dataset
"""
# we already assume 4D images as input
# check if contains dti bval information
bval_tag = Tag(0x0043, 0x1039) # put this there ... | python | def _is_diffusion_imaging(grouped_dicoms):
"""
Use this function to detect if a dicom series is a ge dti dataset
NOTE: We already assume this is a 4D dataset
"""
# we already assume 4D images as input
# check if contains dti bval information
bval_tag = Tag(0x0043, 0x1039) # put this there ... | [
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _4d_to_nifti | def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slic... | python | def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _get_full_block | def _get_full_block(grouped_dicoms):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(grouped_dicoms)):
logger.info('Creating block %s of %s' % (index + 1, len(grouped_dicoms)))
... | python | def _get_full_block(grouped_dicoms):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(grouped_dicoms)):
logger.info('Creating block %s of %s' % (index + 1, len(grouped_dicoms)))
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _get_grouped_dicoms | def _get_grouped_dicoms(dicom_input):
"""
Search all dicoms in the dicom directory, sort and validate them
fast_read = True will only read the headers not the data
"""
# Order all dicom files by InstanceNumber
dicoms = sorted(dicom_input, key=lambda x: x.InstanceNumber)
# now group per st... | python | def _get_grouped_dicoms(dicom_input):
"""
Search all dicoms in the dicom directory, sort and validate them
fast_read = True will only read the headers not the data
"""
# Order all dicom files by InstanceNumber
dicoms = sorted(dicom_input, key=lambda x: x.InstanceNumber)
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _get_bvals_bvecs | def _get_bvals_bvecs(grouped_dicoms):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# loop over all timepoints and create a list with all bvals and bvecs
bvals = numpy.zeros([len(grouped_dicoms)], dtype=numpy.int32)
bvecs = numpy.zeros([len(grouped_dicoms), 3])
for grou... | python | def _get_bvals_bvecs(grouped_dicoms):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# loop over all timepoints and create a list with all bvals and bvecs
bvals = numpy.zeros([len(grouped_dicoms)], dtype=numpy.int32)
bvecs = numpy.zeros([len(grouped_dicoms), 3])
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icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _create_bvals_bvecs | def _create_bvals_bvecs(grouped_dicoms, bval_file, bvec_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# get the bvals and bvecs
bvals, bvecs = _get_bvals_bvecs(grouped_dicoms)
# save the found bvecs to the file
common.write_bval_file(bvals, bval_file)
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"""
Write the bvals from the sorted dicom files to a bval file
"""
# get the bvals and bvecs
bvals, bvecs = _get_bvals_bvecs(grouped_dicoms)
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icometrix/dicom2nifti | dicom2nifti/convert_hitachi.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for hitachi images.
As input hitachi images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the o... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for hitachi images.
As input hitachi images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion function for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
:param output_file: filepath to the output nifti
:param dicom_input: dir... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion function for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
:param output_file: filepath to the output nifti
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _is_mosaic | def _is_mosaic(dicom_input):
"""
Use this function to detect if a dicom series is a siemens 4d dataset
NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory
(containing one series)
"""
# for grouped dicoms
if type(dicom_input) is list and type(d... | python | def _is_mosaic(dicom_input):
"""
Use this function to detect if a dicom series is a siemens 4d dataset
NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory
(containing one series)
"""
# for grouped dicoms
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _mosaic_4d_to_nifti | def _mosaic_4d_to_nifti(dicom_input, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
logger.info('Sorting d... | python | def _mosaic_4d_to_nifti(dicom_input, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _classic_4d_to_nifti | def _classic_4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
all_dicoms = [i fo... | python | def _classic_4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert siemens 4d series to a nifti
Some inspiration on which fields can be used was taken from
http://slicer.org/doc/html/DICOMDiffusionVolumePlugin_8py_source.html
"""
# Get the sorted mosaics
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _classic_get_grouped_dicoms | def _classic_get_grouped_dicoms(dicom_input):
"""
Search all dicoms in the dicom directory, sort and validate them
fast_read = True will only read the headers not the data
"""
# Loop overall files and build dict
# Order all dicom files by InstanceNumber
if [d for d in dicom_input if 'Instan... | python | def _classic_get_grouped_dicoms(dicom_input):
"""
Search all dicoms in the dicom directory, sort and validate them
fast_read = True will only read the headers not the data
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# Loop overall files and build dict
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _classic_get_full_block | def _classic_get_full_block(grouped_dicoms):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(grouped_dicoms)):
logger.info('Creating block %s of %s' % (index + 1, len(grouped_dicom... | python | def _classic_get_full_block(grouped_dicoms):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(grouped_dicoms)):
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _mosaic_get_full_block | def _mosaic_get_full_block(sorted_mosaics):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
for index in range(0, len(sorted_mosaics)):
data_blocks.append(_mosaic_to_block(sorted_mosaics[index]))
# Add... | python | def _mosaic_get_full_block(sorted_mosaics):
"""
Generate a full datablock containing all timepoints
"""
# For each slice / mosaic create a data volume block
data_blocks = []
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _get_sorted_mosaics | def _get_sorted_mosaics(dicom_input):
"""
Search all mosaics in the dicom directory, sort and validate them
"""
# Order all dicom files by acquisition number
sorted_mosaics = sorted(dicom_input, key=lambda x: x.AcquisitionNumber)
for index in range(0, len(sorted_mosaics) - 1):
# Validat... | python | def _get_sorted_mosaics(dicom_input):
"""
Search all mosaics in the dicom directory, sort and validate them
"""
# Order all dicom files by acquisition number
sorted_mosaics = sorted(dicom_input, key=lambda x: x.AcquisitionNumber)
for index in range(0, len(sorted_mosaics) - 1):
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _get_asconv_headers | def _get_asconv_headers(mosaic):
"""
Getter for the asconv headers (asci header info stored in the dicom)
"""
asconv_headers = re.findall(r'### ASCCONV BEGIN(.*)### ASCCONV END ###',
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"""
Getter for the asconv headers (asci header info stored in the dicom)
"""
asconv_headers = re.findall(r'### ASCCONV BEGIN(.*)### ASCCONV END ###',
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _get_mosaic_type | def _get_mosaic_type(mosaic):
"""
Check the extra ascconv headers for the mosaic type based on the slice position
We always assume axial in this case
the implementation resembles the last lines of documentation in
https://www.icts.uiowa.edu/confluence/plugins/viewsource/viewpagesrc.action?pageId=547... | python | def _get_mosaic_type(mosaic):
"""
Check the extra ascconv headers for the mosaic type based on the slice position
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _mosaic_to_block | def _mosaic_to_block(mosaic):
"""
Convert a mosaic slice to a block of data by reading the headers, splitting the mosaic and appending
"""
# get the mosaic type
mosaic_type = _get_mosaic_type(mosaic)
# get the size of one tile format is 64p*64 or 80*80 or something similar
matches = re.find... | python | def _mosaic_to_block(mosaic):
"""
Convert a mosaic slice to a block of data by reading the headers, splitting the mosaic and appending
"""
# get the mosaic type
mosaic_type = _get_mosaic_type(mosaic)
# get the size of one tile format is 64p*64 or 80*80 or something similar
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _create_affine_siemens_mosaic | def _create_affine_siemens_mosaic(dicom_input):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4d if in mosaic format
"""
# read dicom series with pds
dicom_header = dicom_input[0]
# Create affine matrix (http://nipy.sourceforge.net/... | python | def _create_affine_siemens_mosaic(dicom_input):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4d if in mosaic format
"""
# read dicom series with pds
dicom_header = dicom_input[0]
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _create_bvals | def _create_bvals(sorted_dicoms, bval_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
bvals = []
for index in range(0, len(sorted_dicoms)):
if type(sorted_dicoms[0]) is list:
dicom_headers = sorted_dicoms[index][0]
else:
dicom_headers... | python | def _create_bvals(sorted_dicoms, bval_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
bvals = []
for index in range(0, len(sorted_dicoms)):
if type(sorted_dicoms[0]) is list:
dicom_headers = sorted_dicoms[index][0]
else:
dicom_headers... | [
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icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _create_bvecs | def _create_bvecs(sorted_dicoms, bvec_file):
"""
Calculate the bvecs and write the to a bvec file
# inspired by dicom2nii from mricron
# see http://users.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti111.m
"""
if type(sorted_dicoms[0]) is list:
dicom_headers = sorted_dicoms[0][0]
else:... | python | def _create_bvecs(sorted_dicoms, bvec_file):
"""
Calculate the bvecs and write the to a bvec file
# inspired by dicom2nii from mricron
# see http://users.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti111.m
"""
if type(sorted_dicoms[0]) is list:
dicom_headers = sorted_dicoms[0][0]
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icometrix/dicom2nifti | dicom2nifti/resample.py | resample_single_nifti | def resample_single_nifti(input_nifti):
"""
Resample a gantry tilted image in place
"""
# read the input image
input_image = nibabel.load(input_nifti)
output_image = resample_nifti_images([input_image])
output_image.to_filename(input_nifti) | python | def resample_single_nifti(input_nifti):
"""
Resample a gantry tilted image in place
"""
# read the input image
input_image = nibabel.load(input_nifti)
output_image = resample_nifti_images([input_image])
output_image.to_filename(input_nifti) | [
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icometrix/dicom2nifti | dicom2nifti/resample.py | resample_nifti_images | def resample_nifti_images(nifti_images):
"""
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In this calculation we work in 3 spaces / coordinate systems
- original image coordinates
- world coordinates
- "projected" coordinates
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"""
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- original image coordinates
- world coordinates
- "projected" coordinates
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icometrix/dicom2nifti | dicom2nifti/resample.py | _create_affine | def _create_affine(x_axis, y_axis, z_axis, image_pos, voxel_sizes):
"""
Function to generate the affine matrix for a dicom series
This method was based on (http://nipy.org/nibabel/dicom/dicom_orientation.html)
:param sorted_dicoms: list with sorted dicom files
"""
# Create affine matrix (http:... | python | def _create_affine(x_axis, y_axis, z_axis, image_pos, voxel_sizes):
"""
Function to generate the affine matrix for a dicom series
This method was based on (http://nipy.org/nibabel/dicom/dicom_orientation.html)
:param sorted_dicoms: list with sorted dicom files
"""
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icometrix/dicom2nifti | dicom2nifti/convert_dir.py | convert_directory | def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param ou... | python | def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
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icometrix/dicom2nifti | dicom2nifti/convert_dir.py | _is_valid_imaging_dicom | def _is_valid_imaging_dicom(dicom_header):
"""
Function will do some basic checks to see if this is a valid imaging dicom
"""
# if it is philips and multiframe dicom then we assume it is ok
try:
if common.is_philips([dicom_header]):
if common.is_multiframe_dicom([dicom_header]):
... | python | def _is_valid_imaging_dicom(dicom_header):
"""
Function will do some basic checks to see if this is a valid imaging dicom
"""
# if it is philips and multiframe dicom then we assume it is ok
try:
if common.is_philips([dicom_header]):
if common.is_multiframe_dicom([dicom_header]):
... | [
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icometrix/dicom2nifti | dicom2nifti/convert_dir.py | _remove_accents | def _remove_accents(filename):
"""
Function that will try to remove accents from a unicode string to be used in a filename.
input filename should be either an ascii or unicode string
"""
# noinspection PyBroadException
try:
filename = filename.replace(" ", "_")
if isinstance(file... | python | def _remove_accents(filename):
"""
Function that will try to remove accents from a unicode string to be used in a filename.
input filename should be either an ascii or unicode string
"""
# noinspection PyBroadException
try:
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Function that will try to remove accents from a unicode string to be used in a filename.
input filename should be either an ascii or unicode string
"""
if isinstance(filename, type(six.u(''))):
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else:
unicode_filename... | python | def _remove_accents_(filename):
"""
Function that will try to remove accents from a unicode string to be used in a filename.
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.set_border_style | def set_border_style(self, border_style):
"""
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"""
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Set the border style using the specified MenuBorderStyle instance.
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.set_bottom_margin | def set_bottom_margin(self, bottom_margin):
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self.__footer.style.margin... | python | def set_bottom_margin(self, bottom_margin):
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Set the bottom margin of the menu. This will determine the number of console lines appear between the
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.set_left_margin | def set_left_margin(self, left_margin):
"""
Set the left margin of the menu. This will determine the number of spaces between the left edge of the
screen and the left menu border.
:param left_margin: an integer value
"""
self.__header.style.margins.left = left_margin
... | python | def set_left_margin(self, left_margin):
"""
Set the left margin of the menu. This will determine the number of spaces between the left edge of the
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:param left_margin: an integer value
"""
self.__header.style.margins.left = left_margin
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.set_right_margin | def set_right_margin(self, right_margin):
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:param right_margin: an integer value
"""
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Set the right margin of the menu. This will determine the number of spaces between the right edge of the
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:param right_margin: an integer value
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.set_top_margin | def set_top_margin(self, top_margin):
"""
Set the top margin of the menu. This will determine the number of console lines between the top edge
of the screen and the top menu border.
:param top_margin: an integer value
"""
self.__header.style.margins.top = top_margin
... | python | def set_top_margin(self, top_margin):
"""
Set the top margin of the menu. This will determine the number of console lines between the top edge
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:param top_margin: an integer value
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self.__header.style.margins.top = top_margin
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.clear_data | def clear_data(self):
"""
Clear menu data from previous menu generation.
"""
self.__header.title = None
self.__header.subtitle = None
self.__prologue.text = None
self.__epilogue.text = None
self.__items_section.items = None | python | def clear_data(self):
"""
Clear menu data from previous menu generation.
"""
self.__header.title = None
self.__header.subtitle = None
self.__prologue.text = None
self.__epilogue.text = None
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aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.format | def format(self, title=None, subtitle=None, prologue_text=None, epilogue_text=None, items=None):
"""
Format the menu and return as a string.
:return: a string representation of the formatted menu.
"""
self.clear_data()
content = ''
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aegirhall/console-menu | consolemenu/validators/url.py | UrlValidator.validate | def validate(self, input_string):
"""
Validate url
:return: True if match / False otherwise
"""
parsed_url = urlparse(url=input_string)
return bool(parsed_url.scheme and parsed_url.netloc) | python | def validate(self, input_string):
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Validate url
:return: True if match / False otherwise
"""
parsed_url = urlparse(url=input_string)
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.calculate_border_width | def calculate_border_width(self):
"""
Calculate the width of the menu border. This will be the width of the maximum allowable
dimensions (usually the screen size), minus the left and right margins and the newline character.
For example, given a maximum width of 80 characters, with left a... | python | def calculate_border_width(self):
"""
Calculate the width of the menu border. This will be the width of the maximum allowable
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.calculate_content_width | def calculate_content_width(self):
"""
Calculate the width of inner content of the border. This will be the width of the menu borders,
minus the left and right padding, and minus the two vertical border characters.
For example, given a border width of 77, with left and right margins eac... | python | def calculate_content_width(self):
"""
Calculate the width of inner content of the border. This will be the width of the menu borders,
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.inner_horizontal_border | def inner_horizontal_border(self):
"""
The complete inner horizontal border section, including the left and right border verticals.
Returns:
str: The complete inner horizontal border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
... | python | def inner_horizontal_border(self):
"""
The complete inner horizontal border section, including the left and right border verticals.
Returns:
str: The complete inner horizontal border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.outer_horizontal_border_bottom | def outer_horizontal_border_bottom(self):
"""
The complete outer bottom horizontal border section, including left and right margins.
Returns:
str: The bottom menu border.
"""
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... | python | def outer_horizontal_border_bottom(self):
"""
The complete outer bottom horizontal border section, including left and right margins.
Returns:
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.outer_horizontal_border_top | def outer_horizontal_border_top(self):
"""
The complete outer top horizontal border section, including left and right margins.
Returns:
str: The top menu border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
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"""
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aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.row | def row(self, content='', align='left'):
"""
A row of the menu, which comprises the left and right verticals plus the given content.
Returns:
str: A row of this menu component with the specified content.
"""
return u"{lm}{vert}{cont}{vert}".format(lm=' ' * self.margi... | python | def row(self, content='', align='left'):
"""
A row of the menu, which comprises the left and right verticals plus the given content.
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str: A row of this menu component with the specified content.
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aegirhall/console-menu | consolemenu/menu_component.py | MenuItemsSection.show_item_bottom_border | def show_item_bottom_border(self, item_text, flag):
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:param item_text: the text property of the item
:param flag: boolean specifying if the border should be shown.
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aegirhall/console-menu | consolemenu/menu_component.py | MenuItemsSection.show_item_top_border | def show_item_top_border(self, item_text, flag):
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aegirhall/console-menu | consolemenu/format/menu_borders.py | MenuBorderStyleFactory.create_border | def create_border(self, border_style_type):
"""
Create a new MenuBorderStyle instance based on the given border style type.
Args:
border_style_type (int): an integer value from :obj:`MenuBorderStyleType`.
Returns:
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"""
Create a new MenuBorderStyle instance based on the given border style type.
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border_style_type (int): an integer value from :obj:`MenuBorderStyleType`.
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aegirhall/console-menu | consolemenu/format/menu_borders.py | MenuBorderStyleFactory.is_win_python35_or_earlier | def is_win_python35_or_earlier():
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Convenience method to determine if the current platform is Windows and Python version 3.5 or earlier.
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bool: True if the current platform is Windows and the Python interpreter is 3.5 or earlier; False otherwise.
"""
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"""
Convenience method to determine if the current platform is Windows and Python version 3.5 or earlier.
Returns:
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aegirhall/console-menu | consolemenu/items/submenu_item.py | SubmenuItem.set_menu | def set_menu(self, menu):
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Sets the menu of this item.
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:param ConsoleMenu menu: the menu
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Sets the menu of this item.
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aegirhall/console-menu | consolemenu/items/submenu_item.py | SubmenuItem.clean_up | def clean_up(self):
"""
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"""
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self.submenu.join()
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptFormatter.format_prompt | def format_prompt(prompt=None, default=None, enable_quit=False, quit_string='q',
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Format the prompt.
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:param default: the default answer if user does not provide a response.
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.confirm_answer | def confirm_answer(self, answer, message=None):
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.enter_to_continue | def enter_to_continue(self, message=None):
"""
Creates a console prompt with the given message, or defaults to 'Press [Enter] to continue' if no message
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:param message:
"""
if message:
message = message.rstrip() + ' '
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mes... | python | def enter_to_continue(self, message=None):
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.input | def input(self, prompt=None, default=None, validators=None, enable_quit=False, quit_string='q',
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"""
Prompt the user for input.
:param prompt: the message to prompt the user.
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Prompt the user for input.
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.input_password | def input_password(self, message=None):
"""
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"""
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message = self.__prompt_formatter.format_prompt(message)
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.prompt_and_confirm_password | def prompt_and_confirm_password(self, message):
"""
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... | python | def prompt_and_confirm_password(self, message):
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.prompt_for_bilateral_choice | def prompt_for_bilateral_choice(self, prompt, option1, option2):
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"""
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.prompt_for_trilateral_choice | def prompt_for_trilateral_choice(self, prompt, option1, option2, option3):
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.prompt_for_numbered_choice | def prompt_for_numbered_choice(self, choices, title=None, prompt=">"):
"""
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:param title: optional title to display above the numbered list
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aegirhall/console-menu | consolemenu/prompt_utils.py | PromptUtils.validate_input | def validate_input(self, input_string, validators):
"""
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:param validators: the list of validators.
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"""
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aegirhall/console-menu | consolemenu/validators/regex.py | RegexValidator.validate | def validate(self, input_string):
"""
Validate input_string against a regex pattern
:return: True if match / False otherwise
"""
validation_result = False
try:
validation_result = bool(match(pattern=self.pattern, string=input_string))
except TypeError... | python | def validate(self, input_string):
"""
Validate input_string against a regex pattern
:return: True if match / False otherwise
"""
validation_result = False
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validation_result = bool(match(pattern=self.pattern, string=input_string))
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aegirhall/console-menu | consolemenu/multiselect_menu.py | MultiSelectMenu.append_item | def append_item(self, item):
"""
Add an item to the end of the menu before the exit item.
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Args:
item (:obj:`Menu... | python | def append_item(self, item):
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Add an item to the end of the menu before the exit item.
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aegirhall/console-menu | consolemenu/multiselect_menu.py | MultiSelectMenu.process_user_input | def process_user_input(self):
"""
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Examples:
All of the following inputs would have the same result:
* 1,2,3,4
* 1-4
* 1-2,3-4
* 1 -... | python | def process_user_input(self):
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.selected_item | def selected_item(self):
"""
:obj:`consolemenu.items.MenuItem`: The item in :attr:`items` that the user most recently selected, or None.
"""
if self.items and self.selected_option != -1:
return self.items[self.current_option]
else:
return None | python | def selected_item(self):
"""
:obj:`consolemenu.items.MenuItem`: The item in :attr:`items` that the user most recently selected, or None.
"""
if self.items and self.selected_option != -1:
return self.items[self.current_option]
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.append_item | def append_item(self, item):
"""
Add an item to the end of the menu before the exit item.
Args:
item (MenuItem): The item to be added.
"""
did_remove = self.remove_exit()
item.menu = self
self.items.append(item)
if did_remove:
sel... | python | def append_item(self, item):
"""
Add an item to the end of the menu before the exit item.
Args:
item (MenuItem): The item to be added.
"""
did_remove = self.remove_exit()
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.remove_item | def remove_item(self, item):
"""
Remove the specified item from the menu.
Args:
item (MenuItem): the item to be removed.
Returns:
bool: True if the item was removed; False otherwise.
"""
for idx, _item in enumerate(self.items):
if ite... | python | def remove_item(self, item):
"""
Remove the specified item from the menu.
Args:
item (MenuItem): the item to be removed.
Returns:
bool: True if the item was removed; False otherwise.
"""
for idx, _item in enumerate(self.items):
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.remove_exit | def remove_exit(self):
"""
Remove the exit item if necessary. Used to make sure we only remove the exit item, not something else.
Returns:
bool: True if item needed to be removed, False otherwise.
"""
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... | python | def remove_exit(self):
"""
Remove the exit item if necessary. Used to make sure we only remove the exit item, not something else.
Returns:
bool: True if item needed to be removed, False otherwise.
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.start | def start(self, show_exit_option=None):
"""
Start the menu in a new thread and allow the user to interact with it.
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... | python | def start(self, show_exit_option=None):
"""
Start the menu in a new thread and allow the user to interact with it.
The thread is a daemon, so :meth:`join()<consolemenu.ConsoleMenu.join>` should be called if there's a
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.draw | def draw(self):
"""
Refresh the screen and redraw the menu. Should be called whenever something changes that needs to be redrawn.
"""
self.screen.printf(self.formatter.format(title=self.title, subtitle=self.subtitle, items=self.items,
prol... | python | def draw(self):
"""
Refresh the screen and redraw the menu. Should be called whenever something changes that needs to be redrawn.
"""
self.screen.printf(self.formatter.format(title=self.title, subtitle=self.subtitle, items=self.items,
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.process_user_input | def process_user_input(self):
"""
Gets the next single character and decides what to do with it
"""
user_input = self.get_input()
try:
num = int(user_input)
except Exception:
return
if 0 < num < len(self.items) + 1:
self.curren... | python | def process_user_input(self):
"""
Gets the next single character and decides what to do with it
"""
user_input = self.get_input()
try:
num = int(user_input)
except Exception:
return
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.go_down | def go_down(self):
"""
Go down one, wrap to beginning if necessary
"""
if self.current_option < len(self.items) - 1:
self.current_option += 1
else:
self.current_option = 0
self.draw() | python | def go_down(self):
"""
Go down one, wrap to beginning if necessary
"""
if self.current_option < len(self.items) - 1:
self.current_option += 1
else:
self.current_option = 0
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aegirhall/console-menu | consolemenu/console_menu.py | ConsoleMenu.go_up | def go_up(self):
"""
Go up one, wrap to end if necessary
"""
if self.current_option > 0:
self.current_option += -1
else:
self.current_option = len(self.items) - 1
self.draw() | python | def go_up(self):
"""
Go up one, wrap to end if necessary
"""
if self.current_option > 0:
self.current_option += -1
else:
self.current_option = len(self.items) - 1
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aegirhall/console-menu | consolemenu/console_menu.py | ExitItem.show | def show(self, index):
"""
This class overrides this method
"""
if self.menu and self.menu.parent:
self.text = "Return to %s" % self.menu.parent.title
# Check if menu title ends with menu. (Some menus will include Menu in the name).
if not self.text.st... | python | def show(self, index):
"""
This class overrides this method
"""
if self.menu and self.menu.parent:
self.text = "Return to %s" % self.menu.parent.title
# Check if menu title ends with menu. (Some menus will include Menu in the name).
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aegirhall/console-menu | consolemenu/selection_menu.py | SelectionMenu.get_selection | def get_selection(cls, strings, title="Select an option", subtitle=None, exit_option=True, _menu=None):
"""
Single-method way of getting a selection out of a list of strings.
Args:
strings (:obj:`list` of :obj:`str`): The list of strings this menu should be built from.
... | python | def get_selection(cls, strings, title="Select an option", subtitle=None, exit_option=True, _menu=None):
"""
Single-method way of getting a selection out of a list of strings.
Args:
strings (:obj:`list` of :obj:`str`): The list of strings this menu should be built from.
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timothyb0912/pylogit | pylogit/choice_tools.py | get_dataframe_from_data | def get_dataframe_from_data(data):
"""
Parameters
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data : string or pandas dataframe.
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"""
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_object_is_ordered_dict | def ensure_object_is_ordered_dict(item, title):
"""
Checks that the item is an OrderedDict. If not, raises ValueError.
"""
assert isinstance(title, str)
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raise TypeError(msg.format(title, type... | python | def ensure_object_is_ordered_dict(item, title):
"""
Checks that the item is an OrderedDict. If not, raises ValueError.
"""
assert isinstance(title, str)
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_object_is_string | def ensure_object_is_string(item, title):
"""
Checks that the item is a string. If not, raises ValueError.
"""
assert isinstance(title, str)
if not isinstance(item, str):
msg = "{} must be a string. {} passed instead."
raise TypeError(msg.format(title, type(item)))
return None | python | def ensure_object_is_string(item, title):
"""
Checks that the item is a string. If not, raises ValueError.
"""
assert isinstance(title, str)
if not isinstance(item, str):
msg = "{} must be a string. {} passed instead."
raise TypeError(msg.format(title, type(item)))
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_object_is_ndarray | def ensure_object_is_ndarray(item, title):
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_columns_are_in_dataframe | def ensure_columns_are_in_dataframe(columns,
dataframe,
col_title='',
data_title='data'):
"""
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timothyb0912/pylogit | pylogit/choice_tools.py | check_argument_type | def check_argument_type(long_form, specification_dict):
"""
Ensures that long_form is a pandas dataframe and that specification_dict
is an OrderedDict, raising a ValueError otherwise.
Parameters
----------
long_form : pandas dataframe.
Contains one row for each available alternative, fo... | python | def check_argument_type(long_form, specification_dict):
"""
Ensures that long_form is a pandas dataframe and that specification_dict
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_alt_id_in_long_form | def ensure_alt_id_in_long_form(alt_id_col, long_form):
"""
Ensures alt_id_col is in long_form, and raises a ValueError if not.
Parameters
----------
alt_id_col : str.
Column name which denotes the column in `long_form` that contains the
alternative ID for each row in `long_form`.
... | python | def ensure_alt_id_in_long_form(alt_id_col, long_form):
"""
Ensures alt_id_col is in long_form, and raises a ValueError if not.
Parameters
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alt_id_col : str.
Column name which denotes the column in `long_form` that contains the
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_specification_cols_are_in_dataframe | def ensure_specification_cols_are_in_dataframe(specification, dataframe):
"""
Checks whether each column in `specification` is in `dataframe`. Raises
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Parameters
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specification : OrderedDict.
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"""
Checks whether each column in `specification` is in `dataframe`. Raises
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timothyb0912/pylogit | pylogit/choice_tools.py | check_type_and_values_of_specification_dict | def check_type_and_values_of_specification_dict(specification_dict,
unique_alternatives):
"""
Verifies that the values of specification_dict have the correct type, have
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of possible ... | python | def check_type_and_values_of_specification_dict(specification_dict,
unique_alternatives):
"""
Verifies that the values of specification_dict have the correct type, have
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timothyb0912/pylogit | pylogit/choice_tools.py | check_keys_and_values_of_name_dictionary | def check_keys_and_values_of_name_dictionary(names,
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"""
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Parameters
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names : OrderedDict, optional.
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Check the validity of the keys and values in the names dictionary.
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names : OrderedDict, optional.
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_all_columns_are_used | def ensure_all_columns_are_used(num_vars_accounted_for,
dataframe,
data_title='long_data'):
"""
Ensure that all of the columns from dataframe are in the list of used_cols.
Will raise a helpful UserWarning if otherwise.
Parameters
-----... | python | def ensure_all_columns_are_used(num_vars_accounted_for,
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timothyb0912/pylogit | pylogit/choice_tools.py | check_dataframe_for_duplicate_records | def check_dataframe_for_duplicate_records(obs_id_col, alt_id_col, df):
"""
Checks a cross-sectional dataframe of long-format data for duplicate
observations. Duplicate observations are defined as rows with the same
observation id value and the same alternative id value.
Parameters
----------
... | python | def check_dataframe_for_duplicate_records(obs_id_col, alt_id_col, df):
"""
Checks a cross-sectional dataframe of long-format data for duplicate
observations. Duplicate observations are defined as rows with the same
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_num_chosen_alts_equals_num_obs | def ensure_num_chosen_alts_equals_num_obs(obs_id_col, choice_col, df):
"""
Checks that the total number of recorded choices equals the total number of
observations. If this is not the case, raise helpful ValueError messages.
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observations. If this is not the case, raise helpful ValueError messages.
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timothyb0912/pylogit | pylogit/choice_tools.py | check_type_and_values_of_alt_name_dict | def check_type_and_values_of_alt_name_dict(alt_name_dict, alt_id_col, df):
"""
Ensures that `alt_name_dict` is a dictionary and that its keys are in the
alternative id column of `df`. Raises helpful errors if either condition
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alt_name_dict : dict.
A... | python | def check_type_and_values_of_alt_name_dict(alt_name_dict, alt_id_col, df):
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Ensures that `alt_name_dict` is a dictionary and that its keys are in the
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timothyb0912/pylogit | pylogit/choice_tools.py | ensure_ridge_is_scalar_or_none | def ensure_ridge_is_scalar_or_none(ridge):
"""
Ensures that `ridge` is either None or a scalar value. Raises a helpful
TypeError otherwise.
Parameters
----------
ridge : int, float, long, or None.
Scalar value or None, determining the L2-ridge regression penalty.
Returns
------... | python | def ensure_ridge_is_scalar_or_none(ridge):
"""
Ensures that `ridge` is either None or a scalar value. Raises a helpful
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ridge : int, float, long, or None.
Scalar value or None, determining the L2-ridge regression penalty.
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timothyb0912/pylogit | pylogit/choice_tools.py | create_design_matrix | def create_design_matrix(long_form,
specification_dict,
alt_id_col,
names=None):
"""
Parameters
----------
long_form : pandas dataframe.
Contains one row for each available alternative, for each observation.
specifica... | python | def create_design_matrix(long_form,
specification_dict,
alt_id_col,
names=None):
"""
Parameters
----------
long_form : pandas dataframe.
Contains one row for each available alternative, for each observation.
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long_form : pandas dataframe.
Contains one row for each available alternative, for each observation.
specification_dict : OrderedDict.
Keys are a proper subset of the columns in `long_form_df`. Values are
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timothyb0912/pylogit | pylogit/choice_tools.py | get_original_order_unique_ids | def get_original_order_unique_ids(id_array):
"""
Get the unique id's of id_array, in their original order of appearance.
Parameters
----------
id_array : 1D ndarray.
Should contain the ids that we want to extract the unique values from.
Returns
-------
original_order_unique_ids... | python | def get_original_order_unique_ids(id_array):
"""
Get the unique id's of id_array, in their original order of appearance.
Parameters
----------
id_array : 1D ndarray.
Should contain the ids that we want to extract the unique values from.
Returns
-------
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id_array : 1D ndarray.
Should contain the ids that we want to extract the unique values from.
Returns
-------
original_order_unique_ids : 1D ndarray.
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