dataset.py 16.4 KB
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# -*- coding: utf-8 -*-
"""
GEPARD - Gepard-Enabled PARticle Detection
Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program, see COPYING.  
If not, see <https://www.gnu.org/licenses/>.
"""
import os
import pickle
import numpy as np
import cv2
from helperfunctions import cv2imread_fix, cv2imwrite_fix
from copy import copy
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from analysis.particleContainer import ParticleContainer
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currentversion = 3
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def loadData(fname):
    retds = None
    with open(fname, "rb") as fp:
        ds = pickle.load(fp)
        ds.fname = fname
        ds.readin = True
        ds.updatePath()
        retds = DataSet(fname)
        retds.version = 0
        retds.__dict__.update(ds.__dict__)
        if retds.version < currentversion:
            retds.legacyConversion()
        elif retds.zvalimg=="saved":
            retds.loadZvalImg()
    return retds

def saveData(dataset, fname):
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    with open(fname, "wb") as fp:
        # zvalimg is rather large and thus it is saved separately in a tif file 
        # only onces after its creation
        zvalimg = dataset.zvalimg
        if zvalimg is not None:
            dataset.zvalimg = "saved"
        pickle.dump(dataset, fp, protocol=-1)
        dataset.zvalimg = zvalimg
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def arrayCompare(a1, a2):
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    if a1.shape!=a2.shape:
        return False
    if a1.dtype!=np.float32 and a1.dtype!=np.float64:
        return np.all(a1==a2)
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    ind = np.isnan(a1)
    if not np.any(ind):
        return np.all(a1==a2)
    return np.all(a1[~ind]==a2[~ind])

def listCompare(l1, l2):
    if len(l1)!=len(l2):
        return False
    for l1i, l2i in zip(l1, l2):
        if isinstance(l1i, np.ndarray):
            if not isinstance(l2i, np.ndarray) or not arrayCompare(l1i, l2i):
                return False
        elif isinstance(l1i, (list, tuple)):
            if not isinstance(l2i, (list, tuple)) or not listCompare(l1i, l2i):
                return False
        elif l1i!=l2i and ((~np.isnan(l1i)) or (~np.isnan(l2i))):
            return False
    return True

def recursiveDictCompare(d1, d2):
    for key in d1:
        if not key in d2:
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            print("key missing in d2:", key, flush=True)
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            return False
        a = d1[key]
        b = d2[key]
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        print(key, type(a), type(b), flush=True)
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        if isinstance(a, np.ndarray):
            if not isinstance(b, np.ndarray) or not arrayCompare(a, b):
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                print("data is different!", a, b)
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                return False
        elif isinstance(a, dict):
            if not isinstance(b, dict):
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                print("data is different!", a, b)
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                return False
            if not recursiveDictCompare(a, b):
                return False
        elif isinstance(a, (list, tuple)):
            if not isinstance(b, (list, tuple)) or not listCompare(a, b):
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                print("data is different!", a, b)
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                return False
        elif a != b:
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            if (a is not None) and (b is not None):
                print("data is different!", a, b)
                return False
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    return True

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class DataSet(object):
    def __init__(self, fname, newProject=False):
        self.fname = fname
        # parameters specifically for optical scan
        self.version = currentversion
        self.lastpos = None
        self.maxdim = None
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        self.pixelscale_df = None # µm / pixel --> scale of DARK FIELD camera (used for image stitching)
        self.pixelscale_bf = None # µm / pixel of DARK FIELD camera (set to same as bright field, if both use the same camera)
        self.imagedim_bf = None  # width, height, angle of BRIGHT FIELD camera
        self.imagedim_df = None  # width, height, angle of DARK FIELD camera (set to same as bright field, if both use the same camera)
        self.imagescanMode = 'df'    #was the fullimage acquired in dark- or brightfield?
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        self.fitpoints = []   # manually adjusted positions aquired to define the specimen geometry
        self.fitindices = []  # which of the five positions in the ui are already known
        self.boundary = []    # scan boundary computed by a circle around the fitpoints + manual adjustments
        self.grid = []        # scan grid positions for optical scan
        self.zpositions = []  # z-positions for optical scan
        self.heightmap = None
        self.zvalimg = None
        
        # parameters specifically for raman scan
        self.pshift = None    # shift of raman scan position relative to image center
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        self.coordOffset = [0, 0]   #offset of entire coordinate system
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        self.seedpoints = np.array([])
        self.seeddeletepoints = np.array([])
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        self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
                             'contrastcurve': True,
                             'blurRadius': 9,
                             'threshold': 0.2,
                             'maxholebrightness': 0.5,
                             'erodeconvexdefects': 0,
                             'minparticlearea': 20,
                             'minparticledistance': 20,
                             'measurefrac': 1,
                             'compactness': 0.1,
                             'seedRad': 3}
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        self.particleContainer = ParticleContainer(self)
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        self.particleDetectionDone = False
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        self.ramanscandone = False
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        self.resultParams = {'minHQI': 5}
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        self.colorSeed = 'default'
        self.resultsUploadedToSQL = []
        
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        self.readin = True    # a value that is always set to True at loadData 
                              # and mark that the coordinate system might be changed in the meantime
        self.mode = "prepare"
        if newProject:
            self.fname = self.newProject(fname)
        self.updatePath()
        
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    def __eq__(self, other):
        return recursiveDictCompare(self.__dict__, other.__dict__)
        
    def getPixelScale(self, mode=None):
        if mode is None:
            mode = self.imagescanMode
        return (self.pixelscale_df if mode == 'df' else self.pixelscale_bf)
        
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    def saveZvalImg(self):
        if self.zvalimg is not None:
            cv2imwrite_fix(self.getZvalImageName(), self.zvalimg)
            
    def loadZvalImg(self):
        if os.path.exists(self.getZvalImageName()):
            self.zvalimg = cv2imread_fix(self.getZvalImageName(), cv2.IMREAD_GRAYSCALE)
        
    def legacyConversion(self, recreatefullimage=False):
        if self.version==0:
            print("Converting legacy version 0 to 1")
            print("This may take some time")
            
            # local imports as these functions are only needed for the rare occasion of legacy conversion
            from opticalscan import loadAndPasteImage
            
            # try to load png and check for detection contours
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            recreatefullimage = recreatefullimage or not os.path.exists(self.getLegacyImageName())
            if not recreatefullimage:
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                img = cv2imread_fix(self.getLegacyImageName())
                Nc = len(self.particlecontours)
                if Nc>0:
                    contour = self.particlecontours[Nc//2]
                    contpixels = img[contour[:,0,1],contour[:,0,0]]
                    if np.all(contpixels[:,1]==255) and np.all(contpixels[:,2]==0) \
                        and np.all(contpixels[:,0]==0):
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                        recreatefullimage = True
                if not recreatefullimage:
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                    cv2imwrite_fix(self.getImageName(), img)
                del img
            
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            if recreatefullimage:
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                print("recreating fullimage from grid data")
                imgdata = None
                zvalimg = None
                Ngrid = len(self.grid)
                
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                width, height, rotationvalue = self.imagedim_df
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                p0, p1 = self.maxdim[:2], self.maxdim[2:]
                for i in range(Ngrid):
                    print(f"Processing image {i+1} of {Ngrid}")
                    names = []
                    for k in range(len(self.zpositions)):
                        names.append(os.path.join(self.getScanPath(), f"image_{i}_{k}.bmp"))
                    p = self.grid[i]
                    imgdata, zvalimg = loadAndPasteImage(names, imgdata, zvalimg, width, 
                                                            height, rotationvalue, p0, p1, p)
                self.zvalimg = zvalimg
                cv2imwrite_fix(self.getImageName(), cv2.cvtColor(imgdata, cv2.COLOR_RGB2BGR))
                del imgdata
            self.saveZvalImg()
            if "particleimgs" in self.__dict__:
                del self.particleimgs
            
            self.version = 1
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        if self.version == 1:
            print("Converting legacy version 1 to 2")
            if hasattr(self, 'pixelscale'):
                print('pixelscale was', self.pixelscale)
                self.pixelscale_bf = self.pixelscale
                self.pixelscale_df = self.pixelscale
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                del self.pixelscale
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            if hasattr(self, 'imagedim'):
                self.imagedim_bf = self.imagedim
                self.imagedim_df = self.imagedim
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                del self.imagedim
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            if not hasattr(self, 'particles2spectra'):
                self.particles2spectra = [[int(np.where(self.ramanscansortindex == i)[0])] for i in range(len(self.ramanscansortindex))]
            
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            self.version = 2
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        if self.version == 2:
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            print("Converting legacy version 2 to 3")
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            self.particleContainer = ParticleContainer(self)
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            self.particleContainer.initializeParticles(len(self.particlestats))
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            self.particleContainer.setParticleContours(self.particlecontours)
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            self.particleContainer.setParticleStats(self.particlestats)
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            self.particleContainer.applyPixelScaleToParticleStats(self.getPixelScale())
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            self.particleContainer.clearMeasurements()
            
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            if len(self.particlestats) > 0:   #i.e., particle detection was completed and particle data is there 
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                self.particleDetectionDone = True
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                for particleIndex, listOfScanIndices in enumerate(self.particles2spectra):
                    curParticle = self.particleContainer.getParticleOfIndex(particleIndex)
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                    curParticle.measurements = []
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                    for scanIndex in listOfScanIndices:
                        indexOfNewMeas = self.particleContainer.addEmptyMeasurement()
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                        x, y = self.ramanpoints[indexOfNewMeas][0], self.ramanpoints[indexOfNewMeas][1]
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                        self.particleContainer.setMeasurementPixelCoords(indexOfNewMeas, x, y)
                        self.particleContainer.setMeasurementScanIndex(indexOfNewMeas, scanIndex)
                        curParticle.addMeasurement(self.particleContainer.measurements[indexOfNewMeas])
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            for particle in self.particleContainer.particles:
                for meas in particle.measurements:
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                    specIndex = meas.getScanIndex()
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                    meas.setAssignment(self.results['polymers'][specIndex])
                    meas.setHQI(self.results['hqis'][specIndex])
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            self.particleContainer.testForInconsistentParticles()
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            self.version = 3
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        # add later conversion for higher version numbers here
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    def getSubImage(self, img, index, draw=True):
        contour = self.particlecontours[index]
        x0, x1 = contour[:,0,0].min(), contour[:,0,0].max()
        y0, y1 = contour[:,0,1].min(), contour[:,0,1].max()
        subimg = img[y0:y1+1,x0:x1+1].copy()
        if draw:
            cv2.drawContours(subimg, [contour], -1, (0,255,0), 1)
        return subimg
        
    def getZval(self, pixelpos):
        assert self.zvalimg is not None
        zp = self.zvalimg[round(pixelpos[1]), round(pixelpos[0])]
        z0, z1 = self.zpositions.min(), self.zpositions.max()
        return zp/255.*(z1-z0) + z0
        
    def mapHeight(self, x, y):
        assert not self.readin
        assert self.heightmap is not None
        return self.heightmap[0]*x + self.heightmap[1]*y + self.heightmap[2]
        
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    def mapToPixel(self, p, mode='df', force=False):
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        if not force:
            assert not self.readin
        p0 = copy(self.lastpos)
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        if mode == 'df':
            p0[0] -= self.imagedim_df[0]/2
            p0[1] += self.imagedim_df[1]/2
            return (p[0] - p0[0])/self.pixelscale_df, (p0[1] - p[1])/self.pixelscale_df
            
        elif mode == 'bf':
            p0[0] -= self.imagedim_bf[0]/2
            p0[1] += self.imagedim_bf[1]/2
            return (p[0] - p0[0])/self.pixelscale_bf, (p0[1] - p[1])/self.pixelscale_bf
        else:
            print('mapToPixelMode not understood')
            return
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    def mapToLength(self, pixelpos, mode='df', force=False):
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        if not force:
            assert not self.readin
        p0 = copy(self.lastpos)
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        p0[0] += self.coordOffset[0] 
        p0[1] += self.coordOffset[1]
        
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        if mode == 'df':
            p0[0] -= self.imagedim_df[0]/2
            p0[1] += self.imagedim_df[1]/2
            return (pixelpos[0]*self.pixelscale_df + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_df)
        elif mode == 'bf':
            p0[0] -= self.imagedim_bf[0]/2
            p0[1] += self.imagedim_bf[1]/2
            return (pixelpos[0]*self.pixelscale_bf + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_bf)
        else:
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            raise ValueError(f'mapToLength mode: {mode} not understood')
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    def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False):
        p0x, p0y = self.mapToLength(pixelpos, mode = microscopeMode)
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        x, y = p0x + self.pshift[0], p0y + self.pshift[1]
        z = None
        if not noz:
            z = self.mapHeight(x, y)
            z += self.getZval(pixelpos)
        return x, y, z
        
    def newProject(self, fname):
        path = os.path.split(fname)[0]
        name = os.path.splitext(os.path.basename(fname))[0]
        newpath = os.path.join(path, name)
        fname = os.path.join(newpath, name + ".pkl")
        if not os.path.exists(newpath):
            os.mkdir(newpath)        # for new projects a directory will be created
        elif os.path.exists(fname):  # if this project is already there, load it instead
            self.__dict__.update(loadData(fname).__dict__)
        return fname
    
    def getScanPath(self):
        scandir = os.path.join(self.path, "scanimages")
        if not os.path.exists(scandir):
            os.mkdir(scandir)
        return scandir
        
    def updatePath(self):
        self.path = os.path.split(self.fname)[0]
        self.name = os.path.splitext(os.path.basename(self.fname))[0]
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    def getSpectraFileName(self):
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        return os.path.join(self.path, 'spectra.npy')
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    def getImageName(self):
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        return os.path.join(self.path, 'fullimage.tif')

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    def getZvalImageName(self):
        return os.path.join(self.path, "zvalues.tif")
    
    def getLegacyImageName(self):
        return os.path.join(self.path, "fullimage.png")
    
    def getLegacyDetectImageName(self):
        return os.path.join(self.path, "detectimage.png")
    
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    def getBackgroundImageName(self):
        return os.path.join(self.path, "background.bmp")
    
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    def getDetectImageName(self):
        raise NotImplementedError("No longer implemented due to change in API")
    
    def getTmpImageName(self):
        return os.path.join(self.path, "tmp.bmp")
            
    def save(self):
        saveData(self, self.fname)
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    def saveBackup(self):
        inc = 0
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        while True:
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            directory = os.path.dirname(self.fname)
            filename = self.name + '_backup_' + str(inc) + '.pkl'
            path = os.path.join(directory, filename)
            if os.path.exists(path):
                inc += 1
            else:
                saveData(self, path)
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                return filename