class PatchPandas(PatchSimple):
modulename = 'pandas'
input_functions = [
'read_csv', 'read_table', 'read_excel', 'read_hdf', 'read_pickle',
'read_stata', 'read_msgpack'
]
output_functions = [
'DataFrame.to_csv', 'DataFrame.to_excel', 'DataFrame.to_hdf',
'DataFrame.to_msgpack', 'DataFrame.to_stata', 'DataFrame.to_pickle'
]
output_functions += [
'Panel.to_excel', 'Panel.to_hdf', 'Panel.to_msgpack', 'Panel.to_pickle'
]
output_functions += [
'Series.to_csv', 'Series.to_hdf', 'Series.to_msgpack',
'Series.to_pickle'
]
input_wrapper = create_wrapper(log_input, 0, 'pandas')
output_wrapper = create_wrapper(log_output, 0, 'pandas')
add_module_to_db(modulename, input_functions, output_functions)
class PatchGDAL(PatchSimple):
modulename = 'gdal'
input_functions = ['Open']
output_functions = ['Driver.Create', 'Driver.CreateCopy']
input_wrapper = create_wrapper(log_input, 0, 'gdal')
output_wrapper = create_wrapper(log_output, 0, 'gdal')
class PatchPillow(PatchSimple):
modulename = 'PIL'
input_functions = ['Image.open']
output_functions = ['Image.save']
input_wrapper = create_wrapper(log_input, 0, 'Pillow')
output_wrapper = create_wrapper(log_output, 0, 'Pillow')
class PatchSKLearn(PatchSimple):
modulename = 'sklearn'
input_functions = ['datasets.load_svmlight_file']
output_functions = ['datasets.dump_svmlight_file']
input_wrapper = create_wrapper(log_input, 0, 'sklearn')
output_wrapper = create_wrapper(log_output, 0, 'sklearn')
class PatchImageio(PatchSimple):
modulename = 'imageio'
input_functions = ['core.functions.get_reader', 'core.functions.read']
output_functions = ['core.functions.get_writer']
input_wrapper = create_wrapper(log_input, 0, 'imageio')
output_wrapper = create_wrapper(log_output, 0, 'imageio')
class PatchTifffile(PatchSimple):
modulename = 'tifffile'
input_functions = ['imread']
output_functions = ['imsave']
input_wrapper = create_wrapper(log_input, 0, 'tifffile')
output_wrapper = create_wrapper(log_output, 0, 'tifffile')
class PatchBS4(PatchSimple):
modulename = 'bs4'
input_functions = ['BeautifulSoup']
output_functions = []
input_wrapper = create_wrapper(log_input, 0, 'bs4')
output_wrapper = create_wrapper(log_output, 0, 'bs4')
class PatchLXML(PatchSimple):
modulename = 'lxml.etree'
input_functions = ['parse', 'iterparse']
output_functions = []
input_wrapper = create_wrapper(log_input, 0, 'lxml')
output_wrapper = create_wrapper(log_output, 0, 'lxml')
class PatchMPL(PatchSimple):
modulename = 'matplotlib.pyplot'
input_functions = []
output_functions = ['savefig']
input_wrapper = create_wrapper(log_input, 0, 'matplotlib')
output_wrapper = create_wrapper(log_output, 0, 'matplotlib')
class PatchNumpy(PatchSimple):
modulename = 'numpy'
input_functions = ['genfromtxt', 'loadtxt', 'load', 'fromfile']
output_functions = ['save', 'savez', 'savez_compressed', 'savetxt']
input_wrapper = create_wrapper(log_input, 0, 'numpy')
output_wrapper = create_wrapper(log_output, 0, 'numpy')
class PatchNIBabel(PatchSimple):
modulename = 'nibabel'
images = ['nifti1.Nifti1Image', 'nifti2.Nifti2Image', 'freesurfer.mghformat.MGHImage', 'spm99analyze.Spm99AnalyzeImage', 'minc1.Minc1Image', 'minc2.Minc2Image', 'analyze.AnalyzeImage', 'parrec.PARRECImage', 'spm2analyze.Spm2AnalyzeImage']
input_functions = [image_name + '.from_filename' for image_name in images]
output_functions = [image_name + '.to_filename' for image_name in images]
input_wrapper = create_wrapper(log_input, 0, 'nibabel')
output_wrapper = create_wrapper(log_output, 0, 'nibabel')
class PatchSKImage(PatchSimple):
modulename = 'skimage'
input_functions = [
'io.imread', 'io.load_sift', 'io.load_surf', 'external.tifffile.imread'
]
output_functions = ['io.imsave', 'external.tifffile.imsave']
input_wrapper = create_wrapper(log_input, 0, 'sklearn')
output_wrapper = create_wrapper(log_output, 0, 'sklearn')
class PatchNumpy(PatchSimple):
modulename = 'numpy'
# The `load` function is *deliberately* not included here
# as it calls fromfile internally, and then we get two duplicate
# entries recorded in the log
input_functions = ['genfromtxt', 'loadtxt', 'fromfile']
output_functions = ['save', 'savez', 'savez_compressed', 'savetxt']
input_wrapper = create_wrapper(log_input, 0, 'numpy')
output_wrapper = create_wrapper(log_output, 0, 'numpy')
class PatchIris(PatchSimple):
modulename = 'iris'
input_functions = [
'iris.load', 'iris.load_cube', 'iris.load_cubes', 'iris.load_raw'
]
output_functions = ['iris.save']
input_wrapper = create_wrapper(log_input, 0, modulename)
output_wrapper = create_wrapper(log_output, 1, modulename)
add_module_to_db(modulename, input_functions, output_functions)
def add(self, function_names, log_function, arg_loc, modname,
function_type):
if isinstance(function_names, six.string_types):
function_names = [function_names]
wrapper = create_wrapper(log_function, arg_loc, modname)
for f in function_names:
self.functions.append({
'function': f,
'wrapper': wrapper,
'type': function_type
})
