Source code for defdap.inspector

# Copyright 2021 Mechanics of Microstructures Group
#    at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np

import ast

from typing import List

from scipy.stats import linregress
from scipy.stats._stats_mstats_common import LinregressResult
import pandas as pd

from defdap.plotting import Plot, GrainPlot
from defdap import hrdic


[docs]class GrainInspector: """ Class containing the interactive grain inspector tool for slip trace analysis and relative displacement ratio analysis. """ def __init__(self, currMap: 'hrdic.Map', vmax: float = 0.1, corrAngle: float = 0): # Initialise some values self.grainID = 0 self.currMap = currMap self.currEBSDMap = self.currMap.ebsdMap self.currDICGrain = self.currMap[self.grainID] self.currEBSDGrain = self.currDICGrain.ebsdGrain self.vmax = vmax self.corrAngle = corrAngle self.filename = str(self.currMap.retrieveName()) + '_RDR.txt' # Draw the figure self.draw()
[docs] def draw(self): """ Draw the main window, buttons, text boxes and axes. """ # Plot window self.plot = Plot(ax=None, makeInteractive=True, figsize=(14,8), title='Grain Inspector') ######## Buttons self.plot.addButton( 'Save\nLine', self.saveLine, (0.73, 0.48, 0.05, 0.04)) self.plot.addButton( 'Previous\nGrain', lambda e, p: self.gotoGrain(self.grainID-1, p), (0.73, 0.94, 0.05, 0.04)) self.plot.addButton( 'Next\nGrain', lambda e, p: self.gotoGrain(self.grainID+1, p), (0.79, 0.94, 0.05, 0.04)) self.plot.addButton( 'Run\nAll STA', self.batchRunSTA, (0.85, 0.07, 0.11, 0.04)) self.plot.addButton( 'Clear\nAll Lines', self.clearAllLines, (0.89, 0.48, 0.05, 0.04)) self.plot.addButton( 'Load\nFile', self.loadFile, (0.85, 0.02, 0.05, 0.04)) self.plot.addButton( 'Save\nFile', self.saveFile, (0.91, 0.02, 0.05, 0.04)) # Text boxes self.plot.addTextBox(label='', loc=(0.7, 0.02, 0.13, 0.04), changeHandler=self.updateFilename, initial = self.filename) self.plot.addTextBox(label='Go to \ngrain ID:', loc=(0.9, 0.94, 0.05, 0.04), submitHandler=self.gotoGrain) self.plot.addTextBox(label='Remove\nID:', loc=(0.83, 0.48, 0.05, 0.04), submitHandler=self.removeLine) self.RDRGroupBox = self.plot.addTextBox(label='Run RDR only\non group:', loc=(0.78, 0.07, 0.05, 0.04), submitHandler=self.runRDRGroup) # Axes self.maxShearAx = self.plot.addAxes((0.05, 0.4, 0.65, 0.55)) self.slipTraceAx = self.plot.addAxes((0.2, 0.05, 0.6, 0.3)) self.unitCellAx = self.plot.addAxes((0.05, 0.055, 0.15, 0.3), proj='3d') self.grainInfoAx = self.plot.addAxes((0.73, 0.86, 0.25, 0.06)) self.lineInfoAx = self.plot.addAxes((0.73, 0.55, 0.25, 0.3)) self.groupsInfoAx = self.plot.addAxes((0.73, 0.15, 0.25, 0.3)) self.grainPlot = self.currMap[self.grainID].plotMaxShear(fig=self.plot.fig, ax=self.maxShearAx, vmax=self.vmax, plotScaleBar=True, plotColourBar=True) self.plot.ax.axis('off') # Draw the stuff that will need to be redrawn often in a seperate function self.redraw()
[docs] def gotoGrain(self, event: int, plot): """ Go to a specified grain ID. Parameters ---------- event Grain ID to go to. """ ## Go to grain ID specified in event self.grainID=int(event) self.grainPlot.arrow=None self.currDICGrain = self.currMap[self.grainID] self.currEBSDGrain = self.currDICGrain.ebsdGrain self.redraw()
[docs] def saveLine(self, event: np.ndarray, plot): """ Save the start point, end point and angle of drawn line into the grain. Parameters ---------- event Start x, start y, end x, end y point of line passed from drawn line. """ # Get angle of lines lineAngle = 90-np.rad2deg(np.arctan2(self.grainPlot.p2[1]-self.grainPlot.p1[1], self.grainPlot.p2[0]-self.grainPlot.p1[0])) if lineAngle > 180: lineAngle -= 180 elif lineAngle < 0: lineAngle += 180 lineAngle -= self.corrAngle # Two decimal places points = [float("{:.2f}".format(point)) for point in self.grainPlot.p1+self.grainPlot.p2] lineAngle = float("{:.2f}".format(lineAngle)) # Save drawn line to the DIC grain self.currDICGrain.pointsList.append([points, lineAngle, -1]) # Group lines and redraw self.groupLines() self.redrawLine()
[docs] def groupLines(self, grain: 'defdap.hrdic.Grain'=None): """ Group the lines drawn in the current grain item using a mean shift algorithm, save the average angle and then detect the active slip planes. groupsList is a list of line groups: [id, angle, [slip plane id], [angular deviation] Parameters ---------- grain Grain for which to group the slip lines. """ if grain == None: grain = self.currDICGrain if grain.pointsList == []: grain.groupsList = [] else: for i, line in enumerate(grain.pointsList): angle = line[1] if i == 0: line[2]=0 # Make group 0 for first detected angle grain.groupsList = [[0, angle, 0, 0, 0]] nextGroup=1 else: # If there is more that one angle if np.any(np.abs(np.array([x[1] for x in grain.groupsList])-angle)<10): # If within +- 5 degrees of exisitng group, set that as the group group = np.argmin(np.abs(np.array([x[1] for x in grain.groupsList])-angle)) grain.pointsList[i][2]=group newAv = float('{0:.2f}'.format(np.average([x[1] for x in grain.pointsList if x[2]==group]))) grain.groupsList[group][1] = newAv else: # Make new group and set grain.groupsList.append([nextGroup, angle, 0, 0, 0]) line[2]=nextGroup nextGroup += 1 # Detect active slip systems in each group for group in grain.groupsList: activePlanes = [] deviation = [] experimentalAngle = group[1] for idx, theoreticalAngle in enumerate(np.rad2deg(grain.ebsdGrain.slipTraceAngles)): if theoreticalAngle-5 < experimentalAngle < theoreticalAngle+5: activePlanes.append(idx) deviation.append(float('{0:.2f}'.format(experimentalAngle-theoreticalAngle))) group[2] = activePlanes group[3] = deviation
[docs] def clearAllLines(self, event, plot): """ Clear all lines in a given grain. """ self.currDICGrain.pointsList = [] self.currDICGrain.groupsList = [] self.redraw()
[docs] def removeLine(self, event: int, plot): """ Remove single line [runs after submitting a text box]. Parameters ---------- event Line ID to remove. """ ## Remove single line del self.currDICGrain.pointsList[int(event)] self.groupLines() self.redraw()
[docs] def redraw(self): """Draw items which need to be redrawn when changing grain ID. """ # Plot max shear for grain self.maxShearAx.clear() self.grainPlot = self.currMap[self.grainID].plotMaxShear( fig=self.plot.fig, ax=self.maxShearAx, vmax=self.vmax, plotColourBar=False, plotScaleBar=True) # Draw unit cell self.unitCellAx.clear() self.currEBSDGrain.plotUnitCell(fig=self.plot.fig, ax=self.unitCellAx) # Write grain info text self.grainInfoAx.clear() self.grainInfoAx.axis('off') grainInfoText = 'Grain ID: {0} / {1}\n'.format(self.grainID, len(self.currMap.grainList)-1) grainInfoText += 'Min: {0:.1f} % Mean:{1:.1f} % Max: {2:.1f} %'.format( np.min(self.currDICGrain.maxShearList)*100, np.mean(self.currDICGrain.maxShearList)*100, np.max(self.currDICGrain.maxShearList)*100) self.plot.addText(self.grainInfoAx, 0, 1, grainInfoText, va='top', ha='left', fontsize=10) # Detect lines self.plot.addEventHandler('button_press_event',lambda e, p: self.grainPlot.lineSlice(e, p)) self.plot.addEventHandler('button_release_event', lambda e, p: self.grainPlot.lineSlice(e, p)) self.redrawLine()
[docs] def redrawLine(self): """ Draw items which need to be redrawn when adding a line. """ # Write lines text and draw lines linesTxt = 'List of lines\n\nLineID x0 y0 x1 y1 Angle Group\n' if self.currDICGrain.pointsList != []: for idx, points in enumerate(self.currDICGrain.pointsList): linesTxt += '{0} {1:.1f} {2:.1f} {3:.1f} {4:.1f} {5:.1f} {6}\n'.format(idx, points[0][0],points[0][1],points[0][2],points[0][3],points[1],points[2]) self.grainPlot.addArrow(startEnd=points[0], clearPrev=False, persistent=True, label=idx) self.lineInfoAx.clear() self.lineInfoAx.axis('off') self.plot.addText(self.lineInfoAx, 0, 1, linesTxt, va='top', fontsize=10) # Write groups info text groupsTxt = 'List of groups\n\nGroupID Angle System Dev RDR\n' if self.currDICGrain.groupsList != []: for idx, group in enumerate(self.currDICGrain.groupsList): groupsTxt += '{0} {1:.1f} {2} {3} {4:.2f}\n'.format( idx, group[1], group[2], np.round(group[3], 3), group[4]) self.groupsInfoAx.clear() self.groupsInfoAx.axis('off') self.plot.addText(self.groupsInfoAx, 0, 1, groupsTxt, va='top', fontsize=10) # Draw slip traces self.slipTraceAx.clear() self.slipTraceAx.set_aspect('equal', 'box') slipPlot = GrainPlot(fig=self.plot.fig, callingGrain=self.currMap[self.grainID], ax=self.slipTraceAx) traces = slipPlot.addSlipTraces(topOnly=True) self.slipTraceAx.axis('off') # Draw slip bands bands = [elem[1] for elem in self.currDICGrain.groupsList] if self.currDICGrain.groupsList != None: slipPlot.addSlipBands(topOnly=True, angles=list(np.deg2rad(bands)))
[docs] def runRDRGroup(self, event: int, plot): """ Run RDR on a specified group, upon submitting a text box. Parameters ---------- event Group ID specified from text box. """ ## Run RDR for group of lines if event != '': self.calcRDR(grain = self.currDICGrain, group=int(event)) self.RDRGroupBox.set_val('')
[docs] def batchRunSTA(self, event, plot): """ Run slip trace analysis on all grains which hve slip trace lines drawn. """ # Print header print("Grain\tEul1\tEul2\tEul3\tMaxSF\tGroup\tAngle\tSystem\tDev\RDR") # Print information for each grain for idx, grain in enumerate(self.currMap): if grain.pointsList != []: for group in grain.groupsList: maxSF = np.max([item for sublist in grain.ebsdGrain.averageSchmidFactors for item in sublist]) eulers = self.currEBSDGrain.refOri.eulerAngles()*180/np.pi text = '{0}\t{1:.1f}\t{2:.1f}\t{3:.1f}\t{4:.3f}\t'.format( idx, eulers[0], eulers[1], eulers[2], maxSF) text += '{0}\t{1:.1f}\t{2}\t{3}\t{4:.2f}'.format( group[0], group[1], group[2], np.round(group[3],3), group[4]) print(text)
[docs] def calcRDR(self, grain: int, group: int, showPlot: bool = True, length: float = 2.5): """ Calculates the relative displacement ratio for a given grain and group. Parameters ---------- grain DIC grain ID to run RDR on. group group ID to run RDR on. showPlot if True, show plot window. length length of perpendicular lines used for RDR. """ ulist=[]; vlist=[]; allxlist = []; allylist = []; # Get all lines belonging to group points = [] for point in grain.pointsList: if point[2] == group: points.append(point[0]) for point in points: x0=point[0]; y0=point[1]; x1=point[2]; y1=point[3]; grad = (y1-y0)/(x1-x0) invgrad = -1/grad profile_length = np.sqrt((y1-y0)**2+(x1-x0)**2) num = np.round(profile_length*2) ### Calculate positions for each point along slip trace line (x,y) x, y = np.round(np.linspace(x0, x1, int(num))), np.round(np.linspace(y0, y1, int(num))) df = pd.DataFrame({'x':x, 'y':y}).drop_duplicates() x,y = df['x'].values.tolist(),df['y'].values.tolist() ## Calculate deviation from (0,0) for points along line with angle perpendicular to slip line (xnew,ynew) x0new = np.sqrt(length/(invgrad**2+1))*np.sign(grad) y0new = -np.sqrt(length/(1/invgrad**2+1)) x1new = -np.sqrt(length/(invgrad**2+1))*np.sign(grad) y1new = np.sqrt(length/(1/invgrad**2+1)) profile_length=np.sqrt((y1new-y0new)**2+(x1new-x0new)**2) num = np.round(profile_length) xnew, ynew = np.linspace(x0new, x1new, int(num)), np.linspace(y0new, y1new, int(num)) xnew, ynew = np.around(xnew).astype(int), np.around(ynew).astype(int) df = pd.DataFrame({'x':xnew, 'y':ynew}).drop_duplicates() xnew,ynew = df['x'].values.tolist(), df['y'].values.tolist() for x,y in zip(x,y): xperp = []; yperp = []; for xdiff, ydiff in zip(xnew, ynew): xperp.append(int(x+xdiff)) yperp.append(int(y+ydiff)) allxlist.append(xperp) allylist.append(yperp) xmap = self.currDICGrain.extremeCoords[0] + xperp ymap = self.currDICGrain.extremeCoords[1] + yperp ### For all points, append u and v to list u = []; v = []; for xmap, ymap in zip(xmap,ymap): u.append((self.currMap.crop(self.currMap.x_map))[ymap, xmap]) v.append((self.currMap.crop(self.currMap.y_map))[ymap, xmap]) ### Take away mean u = u-np.mean(u); v = v-np.mean(v) ### Append to main lists (ulist,vlist) ulist.extend(u) vlist.extend(v) ### Linear regression of ucentered against vcentered linRegResults = linregress(x=vlist,y=ulist) # Save measured RDR grain.groupsList[group][4] = linRegResults.slope if showPlot: self.plotRDR(grain, group, ulist, vlist, allxlist, allylist, linRegResults)
[docs] def plotRDR(self, grain: int, group: int, ulist: List[float], vlist: List[float], allxlist: List[float], allylist: List[float], linRegResults: 'LinregressResult'): """ Plot RDR figure, including location of perpendicular lines and scatter plot of ucentered vs vcentered. Parameters ---------- grain DIC grain to plot. group Group ID to plot. ulist List of ucentered values. vlist List of vcentered values. allxlist List of all x values. allylist List of all y values. linRegResults Results from linear regression of ucentered vs vcentered {slope, intercept, rvalue, pvalue, stderr}. """ # Draw window and axes self.rdrPlot = Plot(ax=None, makeInteractive=True, title='RDR Calculation', figsize=(21, 7)) self.rdrPlot.ax.axis('off') self.rdrPlot.grainAx = self.rdrPlot.addAxes((0.05, 0.07, 0.20, 0.85)) self.rdrPlot.textAx = self.rdrPlot.addAxes((0.27, 0.07, 0.20, 0.85)) self.rdrPlot.textAx.axis('off') self.rdrPlot.numLineAx = self.rdrPlot.addAxes((0.48, 0.07, 0.2, 0.85)) self.rdrPlot.numLineAx.axis('off') self.rdrPlot.plotAx = self.rdrPlot.addAxes((0.75, 0.07, 0.2, 0.85)) ## Draw grain plot self.rdrPlot.grainPlot = self.currDICGrain.plotMaxShear(fig=self.rdrPlot.fig, ax=self.rdrPlot.grainAx, plotColourBar=False, plotScaleBar = True) self.rdrPlot.grainPlot.addColourBar(label='Effective Shear Strain', fraction=0.046, pad=0.04) ## Draw all points self.rdrPlot.grainAx.plot(allxlist, allylist, 'rx',lw=0.5) for xlist, ylist in zip(allxlist, allylist): self.rdrPlot.grainAx.plot(xlist, ylist, '-',lw=1) ## Generate scatter plot slope = linRegResults.slope r_value = linRegResults.rvalue intercept = linRegResults.intercept std_err = linRegResults.stderr self.rdrPlot.plotAx.scatter(x=vlist,y=ulist,marker='x', lw=1) self.rdrPlot.plotAx.plot( [np.min(vlist), np.max(vlist)],[slope*np.min(vlist)+intercept,slope*np.max(vlist)+intercept], '-') self.rdrPlot.plotAx.set_xlabel('v-centered') self.rdrPlot.plotAx.set_ylabel('u-centered') self.rdrPlot.addText(self.rdrPlot.plotAx, 0.95, 0.01, 'Slope = {0:.3f} ± {1:.3f}\nR-squared = {2:.3f}\nn={3}' .format(slope,std_err,r_value**2,len(ulist)), va='bottom', ha='right', transform=self.rdrPlot.plotAx.transAxes, fontsize=10); ## Write grain info ebsdGrain = grain.ebsdGrain ebsdGrain.calcSlipTraces() if ebsdGrain.averageSchmidFactors is None: raise Exception("Run 'calcAverageGrainSchmidFactors' first") eulers = np.rad2deg(ebsdGrain.refOri.eulerAngles()) text = 'Average angle: {0:.2f}\n'.format(grain.groupsList[group][1]) text += 'Eulers: {0:.1f} {1:.1f} {2:.1f}\n\n'.format(eulers[0], eulers[1], eulers[2]) self.rdrPlot.addText(self.rdrPlot.textAx, 0.15, 1, text, fontsize=10, va='top') ## Write slip system info RDRs = []; offset = 0; for idx, (ssGroup, sfGroup, slipTraceAngle) in enumerate( zip(grain.ebsdMap.slipSystems, ebsdGrain.averageSchmidFactors, np.rad2deg(ebsdGrain.slipTraceAngles))): text = "{0:s} {1:.1f}\n".format(ssGroup[0].slipPlaneLabel, slipTraceAngle) tempRDRs = []; for ss, sf in zip(ssGroup, sfGroup): slipDirSample = ebsdGrain.refOri.conjugate.transformVector(ss.slipDir) text = text + " {0:s} SF: {1:.3f} RDR: {2:.3f}\n".format\ (ss.slipDirLabel, sf,-slipDirSample[0]/slipDirSample[1]) RDR = -slipDirSample[0]/slipDirSample[1] tempRDRs.append(RDR) RDRs.append(tempRDRs) if idx in grain.groupsList[group][2]: self.rdrPlot.addText(self.rdrPlot.textAx, 0.15, 0.9-offset, text, weight='bold', fontsize=10, va='top') else: self.rdrPlot.addText(self.rdrPlot.textAx, 0.15, 0.9-offset, text, fontsize=10, va='top') offset += 0.0275 * text.count('\n') # Plot RDR values on number line uniqueRDRs = set() for x in [item for sublist in RDRs for item in sublist]: uniqueRDRs.add(x) self.rdrPlot.numLineAx.axvline(x=0, ymin=-20, ymax=20, c='k') self.rdrPlot.numLineAx.plot(np.zeros(len(uniqueRDRs)), list(uniqueRDRs), 'bo', label='Theroretical RDR values') self.rdrPlot.numLineAx.plot([0], slope, 'ro', label='Measured RDR value') self.rdrPlot.addText(self.rdrPlot.numLineAx, -0.009, slope-0.01, '{0:.3f}'.format(float(slope))) self.rdrPlot.numLineAx.legend(bbox_to_anchor=(1.15, 1.05)) # Label RDRs by slip system on number line for RDR in list(uniqueRDRs): self.rdrPlot.addText(self.rdrPlot.numLineAx, -0.009, RDR-0.01, '{0:.3f}'.format(float(RDR))) txt = '' for idx, ssGroup in enumerate(RDRs): for idx2, rdr in enumerate(ssGroup): if rdr == RDR: txt += str('{0} {1} '.format(self.currEBSDMap.slipSystems[idx][idx2].slipPlaneLabel, self.currEBSDMap.slipSystems[idx][idx2].slipDirLabel)) self.rdrPlot.addText(self.rdrPlot.numLineAx,0.002, RDR-0.01, txt) self.rdrPlot.numLineAx.set_ylim(slope-1, slope+1) self.rdrPlot.numLineAx.set_xlim(-0.01, 0.05)
[docs] def updateFilename(self, event: str, plot): """ Update class variable filename, based on text input from textbox handler. event: Text in textbox. """ self.filename = event
[docs] def saveFile(self, event, plot): """ Save a file which contains definitions of slip lines drawn in grains [(x0, y0, x1, y1), angle, groupID] and groups of lines, defined by an average angle and identified sip plane [groupID, angle, [slip plane id(s)], [angular deviation(s)]] """ with open(self.currMap.path + str(self.filename), 'w') as file: file.write('# This is a file generated by defdap which contains definitions of slip lines drawn in grains by grainInspector\n') file.write('# [(x0, y0, x1, y1), angle, groupID]\n') file.write('# and groups of lines, defined by an average angle and identified sip plane\n') file.write('# [groupID, angle, [slip plane id], [angular deviation]\n\n') for i, grain in enumerate(self.currMap): if grain.pointsList != []: file.write('Grain {0}\n'.format(i)) file.write('{0} Lines\n'.format(len(grain.pointsList))) for point in grain.pointsList: file.write(str(point)+'\n') file.write('{0} Groups\n'.format(len(grain.groupsList))) for group in grain.groupsList: file.write(str(group)+'\n') file.write('\n')
[docs] def loadFile(self, event, plot): """ Load a file which contains definitions of slip lines drawn in grains [(x0, y0, x1, y1), angle, groupID] and groups of lines, defined by an average angle and identified sip plane [groupID, angle, [slip plane id(s)], [angular deviation(s)]] """ with open(self.currMap.path + str(self.filename), 'r') as file: lines = file.readlines() # Parse file and make list of # [start index, grain ID, number of lines, number of groups] indexlist=[] for i, line in enumerate(lines): if line[0] != '#' and len(line) >1: if ('Grain') in line: grainID = int(line.split(' ')[-1]) startIndex = i if ('Lines') in line: numLines = int(line.split(' ')[0]) if ('Groups') in line: numGroups = int(line.split(' ')[0]) indexlist.append([startIndex, grainID, numLines, numGroups]) # Write data from file into grain for startIndex, grainID, numLines, numGroups in indexlist: startIndexLines = startIndex+2 grainPoints = lines[startIndexLines:startIndexLines+numLines] for point in grainPoints: self.currMap[grainID].pointsList.append(ast.literal_eval(point.split('\\')[0])) startIndexGroups = startIndex+3+numLines grainGroups = lines[startIndexGroups:startIndexGroups+numGroups] for group in grainGroups: self.currMap[grainID].groupsList.append(ast.literal_eval(group.split('\\')[0])) self.redraw()