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How to use shrunk method in hypothesis

Best Python code snippet using hypothesis

xBrepFace_tryGetPrimitiveShape.py

Source:xBrepFace_tryGetPrimitiveShape.py

1"""2190521,22: Import-related update.3190523-24: Added some functions.4190529: Removed a function.5190530-31: Improved printed output.6190605: Fixed a minor bug.7190617: Improved efficiency of a function.8190619: Added a function.9190721: Argument name change.10190722-24: Refactoring.  Changed output of some functions.11190730: More feedback is now returned from a function.12190731: Removed some debug prints.13190809-10: Corrected the default return value in a function.14190822: Modified a comment.15191118-19: Import-related update.16"""1718import Rhino19import Rhino.Geometry as rg20import scriptcontext as sc2122import xPlaneSurface23import xPrimitiveShape242526def tryGetPlane(rgFace0, bMatchToShrunkFace=True, fTolerance=sc.doc.ModelAbsoluteTolerance, bDebug=False):27    28    if bMatchToShrunkFace:29        rgBrep_1Face_Shrunk = rgFace0.DuplicateFace(False)30        rgBrep_1Face_Shrunk.Faces.ShrinkFaces()31        rgFace_Shrunk = rgBrep_1Face_Shrunk.Faces[0]32        rgSrfs_ToTry = rgFace0.UnderlyingSurface(), rgFace_Shrunk.UnderlyingSurface()33    else:34        rgSrfs_ToTry = rgFace0.UnderlyingSurface(),35    36    for i_NotShrunk_Shrunk, rgSrf_ToTry in enumerate(rgSrfs_ToTry):37        rc = xPrimitiveShape.Surface.tryGetPlane(38                rgSrf_ToTry,39                fTolerance=fTolerance,40                bDebug=bDebug)41        if rc[0]:42            if bMatchToShrunkFace: rgBrep_1Face_Shrunk.Dispose()43            rgPlane_Found, fTol_PlaneFound = rc44            if not rgPlane_Found.IsValid:45                return None, "Plane is not valid."46            bShrunkUsed = bool(i_NotShrunk_Shrunk)47            return (rgPlane_Found, fTol_PlaneFound, bShrunkUsed), None48    49    if bMatchToShrunkFace: rgBrep_1Face_Shrunk.Dispose()50    51    return None, "Plane not found within tolerance of {:.2e}.".format(fTolerance)525354def tryGetRoundPrimitive(rgFace0, bMatchToShrunkFace=True, bCylinder=True, bCone=True, bSphere=True, bTorus=True, fTolerance=sc.doc.ModelAbsoluteTolerance, bDebug=False):55    """56    Round primitives are Cone, Cylinder, Sphere, and Torus.57    """58    59    if bDebug:60        reload(xPrimitiveShape)61    62    if bMatchToShrunkFace:63        rgBrep_1Face_Shrunk = rgFace0.DuplicateFace(False)64        rgBrep_1Face_Shrunk.Faces.ShrinkFaces()65        rgFace_Shrunk = rgBrep_1Face_Shrunk.Faces[0]66        rgFaces_ToTest = rgFace0, rgFace_Shrunk67        rgSrfs_ToTry = rgFace0.UnderlyingSurface(), rgFace_Shrunk.UnderlyingSurface()68    else:69        rgSrfs_ToTry = rgFace0.UnderlyingSurface(),70    71    for i_NotShrunk_Shrunk, rgSrf_ToTry in enumerate(rgSrfs_ToTry):72        rc = xPrimitiveShape.Surface.tryGetRoundPrimitive(73                rgSrf0=rgSrf_ToTry,74                bCylinder=bCylinder,75                bCone=bCone,76                bSphere=bSphere,77                bTorus=bTorus,78                fTolerance=fTolerance,79                bDebug=bDebug)80        if rc[0]:81            if bMatchToShrunkFace: rgBrep_1Face_Shrunk.Dispose()82            rgShape_Found, fTol_ShapeFound = rc83            if not rgShape_Found.IsValid:84                return None, "{} is not valid.".format(rgShape_Found.GetType().Name)85            bShrunkUsed = bool(i_NotShrunk_Shrunk)86            return (rgShape_Found, fTol_ShapeFound, bShrunkUsed), None87    88    if bMatchToShrunkFace: rgBrep_1Face_Shrunk.Dispose()89    90    return None, "Round primitive not found within tolerance of {:.2e}.".format(fTolerance)919293def tryGetPlaneSurface(rgFace0, bMatchToShrunkFace=True, fTolerance=0.1*sc.doc.ModelAbsoluteTolerance, bDebug=False):94    """95    Return on success:96        PlaneSurface at a size relative to the BrepFace97        fTol_Used98        bShrunkUsed99    Return on fail:100        None101        String: Log statement.102    """103    104    rgSrf_Face0 = rgFace0.UnderlyingSurface()105    106    if isinstance(rgSrf_Face0, rg.PlaneSurface):107        return None, "Surface is already a PlaneSurface."108    109    rc = tryGetPlane(110            rgFace0,111            bMatchToShrunkFace=bMatchToShrunkFace,112            fTolerance=fTolerance,113            bDebug=bDebug)114    if rc[0] is None:115        return rc116    else:117        rgPlane1, fTol_Used, bShrunkUsed = rc[0]118    119    rgSrf1 = xPlaneSurface.createFromPlaneAndObjectSize(120            rgPlane=rgPlane1,121            obj_ForSize=rgFace0,122            bDebug=bDebug)123    if rgSrf1 is None:124        return None, "createFromPlaneAndObjectSize fail."125    126    return (rgSrf1, fTol_Used, bShrunkUsed), None127128129def tryGetRevSurfaceOfPrimitiveShape(rgFace0, bMatchToShrunkFace=True, bCylinder=True, bCone=True, bSphere=True, bTorus=True, fTolerance=0.1*sc.doc.ModelAbsoluteTolerance, bDebug=False):130    """131    """132    rgSrf0 = rgFace0.UnderlyingSurface()133    134    rc = tryGetRoundPrimitive(135            rgFace0=rgFace0,136            bMatchToShrunkFace=bMatchToShrunkFace,137            bCylinder=bCylinder,138            bCone=bCone,139            bSphere=bSphere,140            bTorus=bTorus,141            fTolerance=fTolerance,142            bDebug=bDebug)143    if rc[0] is None: return None, "No matching primitive shape found."144   145    rgShape1, fTol_PrimitiveMatch, bFoundUsingShunkFace = rc[0]146    147    if isinstance(rgSrf0, rg.RevSurface):148        if isinstance(rgShape1, rg.Cylinder) or isinstance(rgShape1, rg.Cone):149            if rgSrf0.IsClosed(0) or rgSrf0.IsClosed(1):150                return None, "Surface is already a RevSurface of {} shape.".format(rgShape1.GetType().Name)151        152        if isinstance(rgShape1, rg.Sphere) or isinstance(rgShape1, rg.Torus):153            if rgSrf0.IsClosed(0) and rgSrf0.IsClosed(1):154                return None, "Surface is already a RevSurface of {} shape.".format(rgShape1.GetType().Name)155    156    typeShape1 = rgShape1.GetType()157    if not rgShape1.IsValid:158        return None, "{} is not valid.".format(typeShape1)159    160    if typeShape1 == rg.Plane:161        rgPlane = rgShape1162        sType = "Plane"163        rgSrf_Converted = xPlaneSurface.createFromPlaneAndObjectSize(164                rgPlane, rgFace0)165        if rgSrf_Converted is not None:166            return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), None167        else:168            sPrint = 'rgSrf_Converted'169            return None, sPrint + ':', eval(sPrint)170    171    elif typeShape1 == rg.Cylinder:172        rgCyl = rgShape1173        sType = "Cylinder"174        # Fix cylinder that is infinite (has 0 height).175        if not rgCyl.IsFinite:176            if bDebug: print "Making cylinder finite..."177            rgBbox_Face = rgFace0.GetBoundingBox(True)178            fAddLen = 1.1 * rgBbox_Face.Min.DistanceTo(rgBbox_Face.Max)179            rgCyl.Height1 = -fAddLen180            rgCyl.Height2 = fAddLen181        182        183        #    for sAttr in dir(rgCyl):184        #        if (sAttr != 'Unset' and sAttr != '__doc__' and185        #                not callable(getattr(rgCyl, sAttr))):186        #            sPrint = 'rgCyl.' + sAttr; print sPrint + ':', eval(sPrint)187    188    #        sPrint = 'dir(rgCyl)'; print sPrint + ':', eval(sPrint)189        #sPrint = 'rgCyl.Unset'; print sPrint + ':', eval(sPrint)190    #        for sAttr in dir(rgCyl):191    #            if (sAttr != 'Unset' and sAttr != '__doc__' and192    #                    not callable(getattr(rgCyl, sAttr))):193    #                sPrint = 'rgShape1.' + sAttr; print sPrint + ':', eval(sPrint)194        195        elif rgCyl.TotalHeight < 2.0*sc.doc.ModelAbsoluteTolerance:196            if bDebug:197                print "Resultant height of cylinder is {}.".format(198                    rgCyl.TotalHeight)199                print "Using 100 times model's absolute tolerance."200            rgCyl.Height1 = -100.0*sc.doc.ModelAbsoluteTolerance201            rgCyl.Height2 = 100.0*sc.doc.ModelAbsoluteTolerance202        else:203            # Increase length of cylinder so that surface is always larger than trim.204            rgBbox_Face = rgFace0.GetBoundingBox(False)205            rgLines = rgBbox_Face.GetEdges()206            fMaxLen = 0207            for rgLine in rgLines:208                if rgLine.Length > fMaxLen: fMaxLen = rgLine.Length209            fAddLen = 1.1 * fMaxLen210            #fAddLen = 1.1 * rgBbox_Face.Min.DistanceTo(rgBbox_Face.Max)211            rgCyl.Height1 = -fAddLen212            rgCyl.Height2 = fAddLen213        214        rgSrf_Converted = rgCyl.ToRevSurface()215        if rgSrf_Converted is not None:216            return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), None217        else:218            return None, "RevSurface could not be obtained from Cylinder."219        220    elif typeShape1 == rg.Cone:221        rgCone = rgShape1222        sType = "Cone"223        rgSrf_Converted = rgCone.ToRevSurface()224        if rgSrf_Converted is not None:225            return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), None226        else:227            return None, "RevSurface could not be obtained from Cone."228        229        # Increase length of cone so that surface is always larger than trim.230        xf = rg.Transform.Scale(rgCone.ApexPoint, 1.1)231        rgSrf_Converted.Transform(xf)232        233    elif typeShape1 == rg.Sphere:234        rgSphere = rgShape1235        sType = "Sphere"236        rgSrf_Converted = rgSphere.ToRevSurface()237        if rgSrf_Converted is not None:238            return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), None239        else:240            return None, "RevSurface could not be obtained from Sphere."241        242    elif typeShape1 == rg.Torus:243        rgTorus = rgShape1244        sType = "Torus"245        rgSrf_Converted = rgTorus.ToRevSurface()246        if rgSrf_Converted is not None:247            return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), None248        else:249            return None, "RevSurface could not be obtained from Torus."250    251    return None, "What happened?"252    253    s  = "  {} found".format(sType)254    s += " matching {} underlying surface".format(255            "shrunk" if bFoundUsingShunkFace else "full")256    s += " at a tolerance of {}.".format(fTol_PrimitiveMatch)257    258    return (rgSrf_Converted, fTol_PrimitiveMatch, bFoundUsingShunkFace), s259260261def tryGetPrimitiveShape(rgFace0, bMatchToShrunkFace=True, bPlane=True, bCylinder=True, bCone=True, bSphere=True, bTorus=True, fTolerance=1e-9, bDebug=False):262    """263    Updated in May of 2019.  Based on hasPrimitiveShape.264    265    Returns:266        On Success (regardless if primitive is found):267            tuple:268                (269                    tuple: (rg.Plane or rg.Cylinder or rg.Cone or rg.Sphere or rg.Torus,270                    float of tolerance used to find shape,271                    'shrunk' or 'not shrunk')272                ,273                    str: (Fail log)274                )275        On fail: None, None276    """277    rgSrf_Face0 = rgFace0.UnderlyingSurface()278    279280    if bPlane:281        rc = tryGetPlane(282                rgFace0,283                bMatchToShrunkFace=bMatchToShrunkFace,284                fTolerance=fTolerance,285                bDebug=bDebug)286        if rc[0] is not None:287            return rc288289    if bCylinder or bCone or bSphere or bTorus:290        rc = tryGetRoundPrimitive(291                rgFace0=rgFace0,292                bMatchToShrunkFace=bMatchToShrunkFace,293                bCylinder=bCylinder,294                bCone=bCone,295                bSphere=bSphere,296                bTorus=bTorus,297                fTolerance=fTolerance,298                bDebug=bDebug)299        if rc[0] is not None:300            return rc301    302    return None, None
...

bigauto.py

Source:bigauto.py

1#!/usr/bin/env python2# Copyright © 1997, 1999, 2000 Progiciels Bourbeau-Pinard inc.3# François Pinard <pinard@iro.umontreal.ca>, 1997.4"""\5Produce statistics from the results of the bigauto check.6Usage: bigauto [RECODE_OPTION]... [CHARSET_OPTION]...7This script makes a simple analysis for the connectivity of the various8charsets and produce a report on standard output.  The reports include9statistics about the number of steps before and after optimisation.10The option `-hNAME' would affect the resulting output, because there are11more merging rules when this option is in effect.  Other options affect12the result: `-d', `-g' and, notably, `-s'.13All non-option arguments are interpreted as charset names.  If any is given,14the study is limited to those recodings having any of the given charsets15both as a starting and ending points.  If there is no such non-option16argument, all possible possible recodings are considered.17"""18import os, string, sys19def main(*arguments):20    recode_options = []21    charset_options = []22    for argument in arguments:23        if arguments[0] == '-':24            recode_options.append(argument)25        else:26            charset_options.append(argument)27    work_name = '/tmp/bigauto-data'28    if os.path.exists(work_name):29        os.remove(work_name)30    create_data(work_name, recode_options, charset_options)31    report = Report()32    report.digest_data(open(work_name).readline)33    report.produce_report(sys.stdout.write)34    os.remove(work_name)35def create_data(name, recode_options, charset_options):36    # Get the list of charsets.37    if charset_options:38        charsets = charset_options39    else:40        charsets = []41        for line in os.popen('recode -l').readlines():42            charset = string.split(line)[0]43            if charset[0] in ':/':44                continue45            charsets.append(charset)46    # Do the work, calling a subshell once per `before' value.47    recode_call = 'recode </dev/null -v %s' % string.join(recode_options)48    for before in charsets:49        if before in ('count-characters', 'dump-with-names',50                      'flat', 'Texinfo'):51            continue52        sys.stderr.write("Before charset: %s\n" % before)53        write = os.popen('sh >>%s 2>&1' % name, 'w').write54        write('export LANGUAGE; LANGUAGE=C\n'55              'export LANG; LANG=C\n'56              'export LC_ALL; LC_ALL=C\n')57        for after in charsets:58            if after != before:59                write("%s '%s..%s'\n" % (recode_call, before, after))60class Report:61    def __init__(self):62        self.recode_calls = 063        self.original_count = {}64        self.original_example = {}65        self.original_total = 066        self.shrunk_count = {}67        self.shrunk_example = {}68        self.shrunk_total = 069    def digest_data(self, readline):70        lensep = len(os.linesep)71        line = readline()72        while line:73            type, request = string.split(line[:-lensep], ':', 1)74            if type == 'Request':75                steps = self.get_steps(request)76                self.count_original_request(steps, request)77                line = readline()78                if line:79                    if len(string.split(line[:-lensep], ':', 1)) != 2:80                        print '*', line,81                    type, shrunk_to = string.split(line[:-lensep], ':', 1)82                    if type == 'Shrunk to':83                        steps = self.get_steps(shrunk_to)84                        self.count_shrunk_request(steps, shrunk_to)85                        line = readline()86                    else:87                        self.count_shrunk_request(steps, request)88                else:89                    self.count_shrunk_request(steps, request)90            else:91                sys.stderr.write('Unrecognized line: ' + line)92                line = readline()93    def get_steps(self, text):94        if text == '*mere copy*':95            return 096        if text[-1] == '/':97            text = text[:-1]98        text = string.replace(text, '/..', '..')99        count = 0100        for fragment in string.split(text, '..'):101            count = count + len(string.split(fragment, '/'))102        return count - 1103    def count_original_request(self, steps, text):104        self.recode_calls = self.recode_calls + 1105        if self.original_count.has_key(steps):106            self.original_count[steps] = self.original_count[steps] + 1107        else:108            self.original_count[steps] = 1109            self.original_example[steps] = string.strip(text)110            if self.original_total == 0:111                self.original_minimum = self.original_maximum = steps112            else:113                if steps < self.original_minimum:114                    self.original_minimum = steps115                if steps > self.original_maximum:116                    self.original_maximum = steps117        self.original_total = self.original_total + steps118    def count_shrunk_request(self, steps, text):119        if self.shrunk_count.has_key(steps):120            self.shrunk_count[steps] = self.shrunk_count[steps] + 1121        else:122            self.shrunk_count[steps] = 1123            self.shrunk_example[steps] = string.strip(text)124            if self.shrunk_total == 0:125                self.shrunk_minimum = self.shrunk_maximum = steps126            else:127                if steps < self.shrunk_minimum:128                    self.shrunk_minimum = steps129                if steps > self.shrunk_maximum:130                    self.shrunk_maximum = steps131        self.shrunk_total = self.shrunk_total + steps132    def produce_report(self, write):133        if self.recode_calls == 0:134            sys.stderr.write("No call to report\n")135            return136        write("\n"137              "Optimisation     Original  Shrunk\n"138              "              .-------------------\n"139              "Minimum       |  %2d        %2d\n"140              "Maximum       |  %2d        %2d\n"141              "Average       |  %4.1f      %4.1f\n"142              % (self.original_minimum, self.shrunk_minimum,143                 self.original_maximum, self.shrunk_maximum,144                 float(self.original_total) / float(self.recode_calls),145                 float(self.shrunk_total) / float(self.recode_calls)))146        write("\n"147              "Histogram for original requests\n")148        for steps in range(self.original_minimum, self.original_maximum+1):149            if self.original_count.has_key(steps):150                write("%5d steps, %5d times  %s\n"151                      % (steps, self.original_count[steps],152                         self.original_example[steps]))153        write("\n"154              "Histogram for shrunk requests\n")155        for steps in range(self.shrunk_minimum, self.shrunk_maximum+1):156            if self.shrunk_count.has_key(steps):157                write("%5d steps, %5d times  %s\n"158                      % (steps, self.shrunk_count[steps],159                         self.shrunk_example[steps]))160if __name__ == '__main__':...

explore_funcs.py

Source:explore_funcs.py

1import numpy as np 2import pandas as pd 3import scipy as sp4import seaborn as sns5import matplotlib.pyplot as plt6from functools import partial7from jwpy.betabinom import betabinom8def summarize_df(df, head=5, dropna=False):9    '''10    Quick summary of a pandas DataFrame.11    Args:12        df:13        head:14        dropna:15    '''16    # show variable types and numbers of unique levels17    summ = pd.DataFrame(18        [df.dtypes, df.nunique(dropna=dropna), df.isnull().mean(0)],19        index=['dtype', 'nunique', '%missing'])20    # append head21    summ = pd.concat([summ, df.head(head)], axis=0)22    print('{} rows x {} columns'.format(*df.shape))23    return summ24def shrink(values, a, b):25    '''26    Apply empirical Bayes shrinkage to binomial counts for a given Beta prior.27    Args:28        values:29        a:30        b: 31    '''32    zeros, ones = ((values==0).sum(), (values==1).sum())33    return (a + ones)/(a + b + zeros + ones)34def aov_xtab(values, index, columns, figsize=(13, 8), **kwargs):35    '''36    Exploratory plot for pairs of categorical predictors/features.37    Args:38        values:39        index:40        columns:41        figsize:42        kwargs:43    '''44    # group the variables into a DataFrame45    dat = pd.DataFrame({46        'values': values,47        'index': index,48        'columns': columns})49    # fit the beta-binomial model50    endog = pd.DataFrame({51        'k': dat.groupby(['index', 'columns'])['values'].sum(),52        'n': dat.groupby(['index', 'columns'])['values'].count()})53    a, b = betabinom(endog=endog).fit(**kwargs).params54    m = a / (a + b)55    # compute the shrunken cell means and sort the matrix by row/column means56    shrunk = pd.pivot_table(dat, values='values', index='index',57                            columns='columns',58                            aggfunc=partial(shrink, a=a, b=b), fill_value=m)59    new_index = shrunk.index[shrunk.mean(1).argsort()[::-1]]60    new_columns = shrunk.columns[shrunk.mean(0).argsort()[::-1]]61    shrunk = shrunk.reindex_axis(new_index, axis=0)62    shrunk = shrunk.reindex_axis(new_columns, axis=1)63    # compute the numbers of obs. per cell and sort by the same means as above64    annot = pd.crosstab(dat['index'], dat['columns'])65    annot = annot.reindex_axis(new_index, axis=0)66    annot = annot.reindex_axis(new_columns, axis=1)67    # print stuff68    print('SD of row means: {}'.format(shrunk.mean(1).std()))69    print('SD of column means: {}'.format(shrunk.mean(0).std()))70    interaction = shrunk.sub(shrunk.mean(1), axis=0).sub(shrunk.mean(0), axis=1)71    print('SD of row*column interaction: {}'.format(interaction.stack().std()))72    # plot!73    fig, ax = plt.subplots(figsize=figsize)74    return sns.heatmap(shrunk, annot=annot, fmt='.0f');75def shrink_1d(target, group, sort=True, **kwargs):76    '''77    Exploratory plot for pairs of categorical predictors/features.78    Args:79        target: binary (integer or boolean) DV80        group: grouping factor81        sort:82        kwargs:83    '''84    # group the variables into a DataFrame85    dat = pd.DataFrame({86        'target': target,87        'group': group})88    # fit the beta-binomial model89    endog = pd.DataFrame({90        'k': dat.groupby('group')['target'].sum(),91        'n': dat.groupby('group')['target'].count()})92    a, b = betabinom(endog=endog).fit(**kwargs).params93    m = a / (a + b)94    # compute the shrunken cell means and sort the matrix by row/column means95    shrunk = pd.pivot_table(dat, values='values', index='index',96        columns='columns', aggfunc=partial(shrink, a=a, b=b), fill_value=m)97    new_index = shrunk.index[shrunk.mean(1).argsort()[::-1]]98    new_columns = shrunk.columns[shrunk.mean(0).argsort()[::-1]]99    shrunk = shrunk.reindex_axis(new_index, axis=0)100    shrunk = shrunk.reindex_axis(new_columns, axis=1)101    # compute the numbers of obs. per cell and sort by the same means as above102    annot = pd.crosstab(dat['index'], dat['columns'])103    annot = annot.reindex_axis(new_index, axis=0)104    annot = annot.reindex_axis(new_columns, axis=1)105    # print stuff106    print('SD of row means: {}'.format(shrunk.mean(1).std()))107    print('SD of column means: {}'.format(shrunk.mean(0).std()))108    interaction = shrunk.sub(shrunk.mean(1), axis=0).sub(shrunk.mean(0), axis=1)109    print('SD of row*column interaction: {}'.format(interaction.stack().std()))110    # plot!111    fig, ax = plt.subplots(figsize=figsize)...

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