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How to use as_complex method in autotest
Best Python code snippet using autotest_python
curvelet.py
Source:curvelet.py 
1import numpy as np2# -----------------------------------------------------------------------------3# FUNCTION API4# -----------------------------------------------------------------------------5def curvelet_transform(x, num_bands, num_angles = 8, all_curvelets = True, as_complex = False):6 ndims = len(x.shape)7 # This file requires Curvelab and the PyCurveLab packages be installed on your system.8 try:9 import pyct10 except ImportError:11 raise NotImplementedError("Use of curvelets requires installation of CurveLab and the PyCurveLab package.\nSee: http://curvelet.org/ and https://www.slim.eos.ubc.ca/SoftwareLicensed/")12 if ndims == 2:13 ct = pyct.fdct2( n = x.shape,14 nbs = num_bands, # Number of bands15 nba = num_angles, # Number of discrete angles16 ac = all_curvelets,# Return curvelets at the finest detail level17 vec = False, # Return results as nested python vectors18 cpx = as_complex) # Disable complex-valued curvelets19 elif ndims == 3:20 ct = pyct.fdct3( n = x.shape,21 nbs = num_bands, # Number of bands22 nba = num_angles, # Number of discrete angles23 ac = all_curvelets,# Return curvelets at the finest detail level24 vec = False, # Return results as nested python vectors25 cpx = as_complex) # Disable complex-valued curvelets26 else:27 raise NotImplementedError("%dD Curvelets are not supported." % (ndims))28 result = ct.fwd(x)29 del ct30 return result31def inverse_curvelet_transform(coefs, x_shape, num_bands, num_angles, all_curvelets, as_complex):32 # This file requires Curvelab and the PyCurveLab packages be installed on your system.33 try:34 import pyct35 except ImportError:36 raise NotImplementedError("Use of curvelets requires installation of CurveLab and the PyCurveLab package.\nSee: http://curvelet.org/ and https://www.slim.eos.ubc.ca/SoftwareLicensed/")37 if len(x_shape) == 2:38 ct = pyct.fdct2( n = x_shape,39 nbs = num_bands, # Number of bands40 nba = num_angles,41 ac = all_curvelets,42 vec = False,43 cpx = as_complex)44 else:45 ct = pyct.fdct3( n = x_shape,46 nbs = num_bands, # Number of bands47 nba = num_angles,48 ac = all_curvelets,49 vec = False,50 cpx = as_complex)51 result = ct.inv(coefs)52 del ct53 return result54# -----------------------------------------------------------------------------55# OBJECT-ORIENTED API56# -----------------------------------------------------------------------------57class CurveletTransform(object):58 def __init__(self, x_shape, num_bands = None, num_angles = 8, all_curvelets = True, as_complex = False):59 if num_bands == None:60 self._num_bands = int(np.ceil(np.log2(np.min(x_shape)) - 3))61 else:62 self._num_bands = num_bands63 self.x_shape = x_shape64 self.num_angles = num_angles65 self.all_curvelets = all_curvelets66 self.as_complex = as_complex67 self.example_coefs = self.fwd(np.zeros(x_shape))68 # ------------- Forward and inverse transforms ------------------69 def fwd(self, data, num_bands = None):70 '''71 Curvelets must have the num_bands initialized in the72 constructor, but for uniformity with the API for forward73 transforms, we allow the user to supply a num_bands74 argument. If the supplied num_bands does not match the75 num_bands used in the constructor, an error is generated.76 '''77 if num_bands != None:78 assert self._num_bands == num_bands79 # Check argument80 assert data.shape == self.x_shape81 ndims = len(self.x_shape)82 if ndims == 1:83 raise NotImplementedError("1D curvelet transform not yet implemented.")84 elif ndims == 2:85 return curvelet_transform(data, self._num_bands, self.num_angles, self.all_curvelets, self.as_complex)86 elif ndims == 3:87 return curvelet_transform(data, self._num_bands, self.num_angles, self.all_curvelets, self.as_complex)88 else:89 raise NotImplementedError("Curveletes not supported for %dD data." % (len(data.shape)))90 def inv(self, coefs):91 ndims = len(self.x_shape)92 if ndims == 1:93 raise NotImplementedError("1D Inverse curvelet transform not yet implemented.")94 elif ndims == 2:95 return inverse_curvelet_transform(coefs, self.x_shape, self._num_bands, self.num_angles,96 self.all_curvelets, self.as_complex)97 elif ndims == 3:98 return inverse_curvelet_transform(coefs, self.x_shape, self._num_bands, self.num_angles,99 self.all_curvelets, self.as_complex)100 else:101 raise NotImplementedError("Curvelets not supported for %dD data." % (len(data.shape)))102 # --------------------- Utility methods -------------------------103 def num_bands(self, coefs):104 return self._num_bands105 def num_coefficients(self):106 total = 0107 for band in self.example_coefs:108 total += sum([ np.prod(angle.shape) for angle in band ] )109 return total110 def num_nonzero_coefficients(self, coefs):111 total = 0112 for band in coefs:113 total += sum([ angle.nonzero()[0].shape[0] for angle in band ] )114 return total115 def coefs_to_vec(self, coefs):116 return np.hstack([np.hstack([ angle.ravel(order = 'c') for angle in band ]) for band in coefs])117 def vec_to_coefs(self, coef_vec):118 base_idx = 0119 coefs = []120 for band in self.example_coefs:121 angle_list = []122 for angle in band:123 angle_size = np.prod(angle.shape)124 angle_list.append(np.reshape(coef_vec[base_idx:base_idx+angle_size], angle.shape, order = 'c'))125 base_idx += angle_size126 coefs.append(angle_list)127 return coefs128 def update(self, coefs, update, alpha):129 '''130 Adds the update (multiplied by alpha) to each set of131 coefficients.132 '''133 delta_sqrsum = 0.0134 for band in xrange(len(coefs)):135 for angle in xrange(len(coefs[band])):136 delta = alpha * update[band][angle]137 coefs[band][angle] += delta138 delta_sqrsum += np.square(delta).sum()139 update_norm = np.sqrt(delta_sqrsum)140 return (coefs, update_norm)141 def mean(self, coefs):142 '''143 Compute the average over all wavelet coefficients.144 '''145 accum = []146 for coef in coefs:147 accum.append(np.hstack( [ block.ravel() for block in coef ] ))148 return np.hstack(accum).mean()149 # ------------------ Thresholding methods -----------------------150 def _estimate_noise(self):151 '''152 Helper function for the thresholding function below.153 Adapted from the fdct_osfft_demo_denoise.m file in CurveLab.154 '''155 E_coefs = self.fwd(np.random.randn(*self.x_shape))156 E_thresholds = []157 for band in xrange(len(E_coefs)):158 angle_thresholds = []159 for angle in xrange(len(E_coefs[band])):160 A = E_coefs[band][angle]161 angle_thresholds.append( np.median(np.abs(A - np.median(A)))/0.6745 )162 E_thresholds.append(angle_thresholds)163 return E_thresholds164 def threshold_by_band(self, coefs, threshold_func, skip_bands = [], within_axis = None, scaling_factor = None):165 '''166 Threshold each band individually. The threshold_func() should167 take an array of coefficients (which may be 1d or 2d or 3d),168 and return a tuple: (band_center, band_threshold)169 For the sake of speed and memory efficiency, updates to the coefficients170 are performed in-place.171 '''172 # Skip the lowest frequency band173 for b in xrange(1, len(coefs)):174 num_removed = 0175 num_total = 0176 # Skip band?177 if b in skip_bands:178 continue179 # print num_total - num_removed, num_total180 # Compute the center and threshold.181 tmp = np.hstack( [ angle.ravel() for angle in coefs[b] ] )182 (band_center, band_threshold) = threshold_func(tmp, b, None)183 # print '\t\t****', b, band_center, band_threshold184 #if scaling_factor != None:185 # band_threshold /= scaling_factor186 for a in xrange(len(coefs[b])):187 # Soft threshold the coefficients188 idxs = np.where( coefs[b][a] > band_threshold )189 coefs[b][a][idxs] -= band_threshold190 idxs = np.where( np.abs(coefs[b][a]) <= band_threshold )191 coefs[b][a][idxs] = 0.0192 idxs = np.where( coefs[b][a] < -band_threshold )193 coefs[b][a][idxs] += band_threshold194 #idxs = np.where( np.abs( coefs[b][a] - band_center ) < band_threshold )# * scaling_factor[b][a] / max_scale )195 #num_removed += idxs[0].shape[0]196 #num_total += np.prod(coefs[b][a].shape)197 #coefs[b][a][idxs] = 0.0198 #print 'Retained %0.2f -- ( %g / %g )' % (100.0*(num_total - num_removed)/float(num_total),199 # num_total - num_removed, num_total)...
test_api.py
Source:test_api.py
1#!/usr/bin/env python2# -*- coding: utf-8 -*-3#4# parselglossy -- Generic input parsing library, speaking in tongues5# Copyright (C) 2020 Roberto Di Remigio, Radovan Bast, and contributors.6#7# This file is part of parselglossy.8#9# Permission is hereby granted, free of charge, to any person obtaining a copy10# of this software and associated documentation files (the "Software"), to deal11# in the Software without restriction, including without limitation the rights12# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell13# copies of the Software, and to permit persons to whom the Software is14# furnished to do so, subject to the following conditions:15#16# The above copyright notice and this permission notice shall be included in17# all copies or substantial portions of the Software.18#19# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR20# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,21# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE22# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER23# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,24# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE25# SOFTWARE.26#27# For information on the complete list of contributors to the28# parselglossy library, see: <http://parselglossy.readthedocs.io/>29#30"""Tests for `parselglossy` package."""31import json32from pathlib import Path33from shutil import rmtree34import pytest35from parselglossy import api36from parselglossy.utils import as_complex37@pytest.mark.parametrize(38 "args,out,reference",39 [40 (("tests/api/standard.inp",), None, "tests/ref/standard_ir.json"),41 (42 ("tests/api/scf.inp", "standard", "scf_ir.json"),43 "scf_ir.json",44 "tests/ref/scf_ir.json",45 ),46 (47 ("tests/api/getkw.inp", "getkw", "lex_ir.json"),48 "lex_ir.json",49 "tests/ref/getkw_ir.json",50 ),51 ],52 ids=["lex-default", "lex-standard-w-outfile", "lex-getkw-w-outfile"],53)54def test_api_lex(args, out, reference):55 ir = api.lex(*args)56 # Check intermediate representation matches with reference57 ref_json = Path(reference).resolve()58 if out is None:59 with ref_json.open("r") as f:60 assert ir == json.loads(f.read(), object_hook=as_complex)61 else:62 dumped = Path(out).resolve()63 with ref_json.open("r") as ref, dumped.open("r") as o:64 assert json.loads(o.read(), object_hook=as_complex) == json.loads(65 ref.read(), object_hook=as_complex66 )67 # Clean up JSON file68 dumped.unlink()69@pytest.mark.parametrize(70 "args,out,reference",71 [72 (73 ("tests/ref/scf_ir.json", "tests/validation/overall/template.yml"),74 None,75 "tests/ref/scf_fr.json",76 ),77 (78 (79 "tests/ref/scf_ir.json",80 "tests/validation/overall/template.yml",81 "scf_fr.json",82 ),83 "scf_fr.json",84 "tests/ref/scf_fr.json",85 ),86 ],87 ids=["validate-default", "validate-w-outfile"],88)89def test_api_validate(args, out, reference):90 fr = api.validate(*args)91 # Check final representation matches with reference92 ref_json = Path(reference).resolve()93 if out is None:94 with ref_json.open("r") as f:95 assert fr == json.loads(f.read(), object_hook=as_complex)96 else:97 dumped = Path(out).resolve()98 with ref_json.open("r") as ref, dumped.open("r") as o:99 assert json.loads(o.read(), object_hook=as_complex) == json.loads(100 ref.read(), object_hook=as_complex101 )102 # Clean up JSON file103 dumped.unlink()104@pytest.mark.parametrize(105 "args,out,reference",106 [107 (108 ("tests/api/scf.inp", "tests/validation/overall/template.yml"),109 None,110 "tests/ref/scf_fr.json",111 ),112 (113 (114 "tests/api/scf.inp",115 "tests/validation/overall/template.yml",116 "scf_fr.json",117 ),118 "scf_fr.json",119 "tests/ref/scf_fr.json",120 ),121 (122 (123 "tests/api/scf.inp",124 "tests/validation/overall/template.yml",125 None,126 "standard",127 True,128 ),129 None,130 "tests/ref/scf_fr.json",131 ),132 ],133 ids=["parse-default", "parse-w-outfile", "parse-w-dumpir"],134)135def test_api_parse(args, out, reference):136 fr = api.parse(*args)137 # Check final representation matches with reference138 ref_json = Path(reference).resolve()139 if out is None:140 with ref_json.open("r") as f:141 assert fr == json.loads(f.read(), object_hook=as_complex)142 else:143 dumped = Path(out).resolve()144 with ref_json.open("r") as ref, dumped.open("r") as o:145 assert json.loads(o.read(), object_hook=as_complex) == json.loads(146 ref.read(), object_hook=as_complex147 )148 # Clean up JSON file149 dumped.unlink()150@pytest.mark.parametrize(151 "args,out,reference",152 [153 (("tests/api/docs_template.yml",), None, "tests/ref/input.rst"),154 (155 ("tests/api/docs_template.yml", "input.rst"),156 "input.rst",157 "tests/ref/input.rst",158 ),159 (160 (161 "tests/api/docs_template.yml",162 "input.rst",163 "Dwigt Rortugal's guide to input parameters",164 ),165 "input.rst",166 "tests/ref/dwigt.rst",167 ),168 ],169 ids=["document-default", "document-w-outfile", "document-w-header"],170)171def test_api_document(args, out, reference):172 docs = api.document(*args)173 # Check final representation matches with reference174 ref_rst = Path(reference).resolve()175 if out is None:176 with ref_rst.open("r") as ref:177 assert docs == ref.read()178 else:179 dumped = Path(out).resolve()180 with ref_rst.open("r") as ref, dumped.open("r") as o:181 assert o.read() == ref.read()182 # Clean up .rst file183 dumped.unlink()184@pytest.mark.parametrize(185 "args,inp,references",186 [187 (188 {189 "template": "tests/validation/overall/template.yml",190 "docfile": "foo.rst",191 "grammar": "standard",192 },193 "tests/api/scf.inp",194 ("tests/ref/scf_fr.json", "tests/ref/generated_input.rst"),195 ),196 (197 {198 "template": "tests/validation/overall/template.yml",199 "docfile": "babar.rst",200 "grammar": [201 Path(__file__).parents[1].absolute()202 / f"parselglossy/grammars/{x}.py"203 for x in ["atoms", "getkw"]204 ],205 "tokenize": "from . import getkw; lexer = getkw.grammar(has_complex=True); ir = lexer.parseString(in_str).asDict()",206 },207 "tests/api/scf.inp",208 ("tests/ref/scf_fr.json", "tests/ref/generated_input.rst"),209 ),210 ],211 ids=["generate-default", "generated-custom-grammar"],212)213def test_api_generate(args, inp, references):214 # generate parser215 parser_dir = api.generate(**args)216 # use generated parser to parse inp217 from input_parser import api as generated_api218 fr = generated_api.parse(inp)219 # Check final representation matches with reference220 ref_json = Path(references[0]).resolve()221 with ref_json.open("r") as ref:222 assert fr == json.loads(ref.read(), object_hook=as_complex)223 # Check generated documentation agrees with reference224 ref_rst = Path(references[1]).resolve()225 dumped = parser_dir / f"docs/{args['docfile']}"226 with ref_rst.open("r") as ref, dumped.open("r") as o:227 assert o.read() == ref.read()228 # clean up generated parser...
conversions.py
Source:conversions.py
1def int_to_str(value, width):2 """3 Outputs a string of the binary of the value with4 LSB to the left.5 """6 s = bin(value)[2:]7 assert len(s) <= width8 s = '0' * (width - len(s)) + s9 return s10def signed_to_slv(value, width):11 """12 Takes a value between -1 to 1 inclusive and maps it13 into `width` bits.14 >>> bin(signed_to_slv(1, 8))15 '0b1000000'16 >>> bin(signed_to_slv(-1, 8))17 '0b11000000'18 """19 assert abs(value) <= 120 max_mag = pow(2, width-2)21 scaled = round(value * max_mag)22 if scaled < 0:23 scaled = pow(2, width) + scaled24 assert scaled < pow(2, width)25 assert isinstance(scaled, int)26 return scaled27def slv_to_signed(value, width):28 max_mag = pow(2, width-2)29 if value >= pow(2, width-1):30 value = value - pow(2, width)31 scaled = value / max_mag32 assert scaled <= 133 return scaled34def complex_to_slv(value, width):35 """36 Maps a complex number, `value`, (with mag <= 1) to an integer with37 bit width of width `width`.38 >>> bin(complex_to_slv(1+0j, 12))39 '0b10000000000'40 >>> bin(complex_to_slv(0.5-0.5j, 12))41 '0b1000111000'42 """43 assert width % 2 == 044 assert abs(value) <= 145 mapped_real = signed_to_slv(value.real, width//2)46 mapped_imag = signed_to_slv(value.imag, width//2)47 mapped = mapped_imag + mapped_real * pow(2, width//2)48 return mapped49def complex_from_slv(value, width):50 """51 Maps an integer (with bit-width `width`)52 to a complex number.53 """54 assert value < pow(2, width)55 assert width % 2 == 056 real_part = value >> width//257 imag_part = value % pow(2, width//2)58 imag_float = slv_to_signed(imag_part, width//2)59 real_float = slv_to_signed(real_part, width//2)60 as_complex = real_float + imag_float * (0+1j)61 return as_complex62def list_of_complex_to_slv(values, width):63 slv = 064 f = 165 for value in values:66 slv += complex_to_slv(value, width) * f67 f = f << width68 return slv69def list_of_complex_from_slv(value, width, size):70 assert value < pow(2, width*size)71 bits = ''.join(reversed(bin(value)[2:]))72 assert len(bits) <= width * size73 bits += '0' * (width*size - len(bits))74 lumps = [bits[index*width: (index+1)*width]75 for index in range(size)]76 complexes = []77 for lump in lumps:78 as_int = int(''.join(reversed(lump)), 2)79 as_complex = complex_from_slv(as_int, width)80 complexes.append(as_complex)81 return complexes82def list_of_uints_to_slv(values, width):83 slv = 084 f = 185 step = pow(2, width)86 for value in values:87 slv += value * f88 f *= step89 return slv90def list_of_uints_from_slv(slv, width, size):91 step = pow(2, width)92 values = []93 for i in range(size):94 values.append(slv % step)95 slv = slv >> width96 assert slv == 097 return values98if __name__ == '__main__':99 import doctest...
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