def getSaveFileName(self, *args, **kwargs):
"""
analogue to QtWidgets.QFileDialog.getSaveFileNameAndFilter
but returns the filename + chosen file ending even if not typed in gui
"""
if 'directory' not in kwargs:
if self.opts['save']:
if self.opts['save']:
kwargs['directory'] = self.opts['save']
fname = QtWidgets.QFileDialog.getSaveFileName(**kwargs)
if fname:
if type(fname) == tuple:
# only happened since qt5
# getSaveFileName returns (path, ftype)
if not fname[0]:
return
p = PathStr(fname[0])
if not p.filetype():
ftyp = self._extractFtype(fname[1])
p = p.setFiletype(ftyp)
else:
p = PathStr(fname)
self.opts['save'] = p.dirname()
if self.opts['open'] is None:
self.opts['open'] = self.opts['save']
return p
def _getLayerLabel(fname, label):
if fname is None:
if label is None:
return 'unknown'
return label
if PathStr(fname).isfile():
fname = PathStr(fname).basename()
if label is not None:
return '%s - %s' % (label, fname)
return fname
def getOpenFileNames(self, **kwargs):
kwargs = self._processOpenKwargs(kwargs)
fnames = QtWidgets.QFileDialog.getOpenFileNames(**kwargs)
# PyQt4 and 5 comp. workaround
if isinstance(fnames, tuple) and isinstance(fnames[0], list):
fnames = fnames[0]
for n, f in enumerate(fnames):
fnames[n] = PathStr(f)
if fnames:
self.opts['open'] = PathStr(f).dirname()
return fnames
def pathJoin(pathlist):
if len(pathlist) > 5:
mod, number, name, current, date = pathlist[:5]
date = date.replace(':', '-')
dd0 = '__'.join((number, name))
dd1 = '__'.join((current, date))
out = PathStr(mod).join(dd0, dd1)
if len(pathlist[5:]):
out = out.join(*tuple(pathlist[5:]))
return out
return PathStr(pathlist[0]).join(*pathlist[1:])
def pathJoin(pathlist):
if len(pathlist) > 5:
mod, number, name, current, date = pathlist[:5]
# date = date.replace(':', '-')
date = datetime.strptime(date, '%x %X').strftime("%Y-%m-%dT%H_%M_%S")
dd0 = '__'.join((number, name))
dd1 = '__'.join((current, date))
out = PathStr(mod).join(dd0, dd1)
if len(pathlist[5:]):
out = out.join(*tuple(pathlist[5:]))
return out
return PathStr(pathlist[0]).join(*pathlist[1:])
def _pathToData(self, rootpath):
'''returns 2d array of all files in [rootpath], splitted by folder'''
self._root = rootpath
f = list(PathStr(rootpath).nestedFiles(includeroot=False))
f = [fi for fi in f if not fi.isHidden()]
data = [self.pathSplit(fi) for fi in f]
dates = [dateStr(rootpath.join(fi).date()) for fi in f]
sizes = [fs.toStr(rootpath.join(fi).size()) for fi in f]
# transform list of lists into array:
# lmax = max([len(d) for d in data])
data2 = np.zeros(shape=(len(data), self.columnCount()),
dtype="<U%i" % self.STRING_LEN)
pathindices = np.array([self.col(ni) for ni in range(self._n)])
fileindex = self.col(self._n)
sizeindex = self.col(self._n + 3)
dateindex = self.col(self._n + 1)
for (dd, d2, date, size) in zip(data, data2, dates, sizes):
# if 'DATA' in dd:
# print(dd)
d2[pathindices[:len(dd) - 1]] = dd[:-1]
d2[fileindex] = dd[-1]
d2[sizeindex] = size
d2[dateindex] = date
return data2
def _changeRootPath(self):
r = self.gui.root # self.fileTableView.rootPath()
new_r = QtWidgets.QFileDialog.getExistingDirectory(directory=r)
if new_r:
self.gui.setProjectFolder(PathStr(new_r))
self.fileTableView.rootPathChanged(False) # (PathStr(new_r))
self._updateFilePathLabel()
def vignettingFromRandomSteps(imgs, bg, inPlane_scale_factor=None,
debugFolder=None, **kwargs):
'''
important: first image should shown most iof the device
because it is used as reference
'''
# TODO: inPlane_scale_factor
if debugFolder:
debugFolder = PathStr(debugFolder)
s = ObjectVignettingSeparation(imgs[0], bg, **kwargs)
for img in imgs[1:]:
fit = s.addImg(img)
if debugFolder and fit is not False:
imwrite(debugFolder.join('fit_%s.tiff' % len(s.fits)), fit)
if debugFolder:
imwrite(debugFolder.join('init.tiff'), s.flatField)
smoothed_ff, mask, flatField, obj = s.separate()
if debugFolder:
imwrite(debugFolder.join('object.tiff'), obj)
imwrite(debugFolder.join('flatfield.tiff'), flatField, dtype=float)
imwrite(debugFolder.join('flatfield_smoothed.tiff'), smoothed_ff,
dtype=float)
return smoothed_ff, mask
def fillFromState(self, lines, appendRows=False):
self._allowModelToModifyCells = False
if appendRows:
row0 = self.rowCount()
else:
row0 = 0
self.clearContents()
self.paths = []
nrows = row0 + len(lines)
self.setRowCount(nrows)
self._new_rows = []
for row, line in enumerate(lines):
row += row0
for col, txt in enumerate(line):
if txt != '':
self.setCell(row, col, txt)
item = self.item(row, 0)
if len(line) and item:
self.paths.append(PathStr(item.text()))
self._setPathItem(row)
self._setRowItem(row)
self._new_rows.append(row)
else:
nrows -= 1
self.drawWidget.setExamplePath(self.paths[0])
self.setRowCount(nrows)
self._checkShowOptionsColumn()
self._new_paths = self.paths[row0:]
self.filled.emit()
def addFilePath(self, filepath):
'''
create a new display for one ore more given file paths
INPUT: "Path/To/File.txt"
'''
if filepath:
return self.currentWorkspace().addFiles([PathStr(filepath)])
def getExistingDirectory(self, **kwargs):
kwargs = self._processOpenKwargs(kwargs)
fname = QtWidgets.QFileDialog.getExistingDirectory(**kwargs)
if fname:
p = PathStr(fname)
self.opts['open'] = p.dirname()
return p
def html2data(html):
'''
extract either tables or images from html code
'''
paths = []
# data = []
doc = lxml.html.fromstring(html)
#images in html
for img in doc.cssselect("img"): #doc.xpath('img'):
# get the scr-path of the image:
imgsrc = img.get('src')
fname = PathStr(imgsrc).basename()
if not hasattr(html2data, 'TMP_IMG_DIR'):
html2data.TMP_IMG_DIR = PathStr(tempfile.mkdtemp('tmpImgDir'))
fpath = html2data.TMP_IMG_DIR.join(fname)
#in case img src is within HTML code:
if not fname.filetype():
ftype = imgsrc[imgsrc.index('image/') + 6:imgsrc.index(';')]
fpath = fpath.setFiletype(ftype)
# download the image in a temporary folder:
urllib.request.urlretrieve(imgsrc, fpath)
paths.append(fpath)
#TODO: doesnt work and table import from internet
#...is not really needed
# # tables
# table = _html2PyTable(doc)
# if table:
# data.append(table)
return paths #, data
# def _html2PyTable(doc):
# table = []
# try:
# rows = doc.cssselect("tr")
# # TODO:
# except: # lxml.cccselect uses __import__ which doesnt work with pyinstaller
# print('dynamic import error in lxml.cccselect')
# return []
# for row in rows:
# table.append(list())
# for td in row.cssselect("td"):
# table[-1].append(str(td.text_content()))
# return table
def _copyToNewFolder(self):
f = QtWidgets.QFileDialog.getExistingDirectory()
if f:
m = self.selectionModel()
for index in m.selectedRows():
y = index.row()
path = self._path2(y)
self._root.join(path).copy(PathStr(f).join(path.basename()))
QtGui.QDesktopServices.openUrl(QtCore.QUrl(f))
def getOpenFileName(self, **kwargs):
kwargs = self._processOpenKwargs(kwargs)
fname = QtWidgets.QFileDialog.getOpenFileName(**kwargs)
if isinstance(fname, tuple):
fname = fname[0]
if fname:
p = PathStr(fname)
self.opts['open'] = p.dirname()
return p
def plotFitResult(fit,
show_legend=True,
show_plots=True,
save_to_file=False,
foldername='',
filename='',
filetype='png'):
from matplotlib import pyplot
xvals = fit.xvals
yvals = fit.yvals
fit = fit.fitValues(xvals)
fig, ax = pyplot.subplots(1)
ax.plot(xvals, yvals, label='histogram', linewidth=3)
for n, f in enumerate(fit):
ax.plot(xvals, f, label='peak %i' % (n + 1), linewidth=6)
l2 = ax.legend(loc='upper center',
bbox_to_anchor=(0.7, 1.05),
ncol=3,
fancybox=True,
shadow=True)
l2.set_visible(show_legend)
pyplot.xlabel('pixel value')
pyplot.ylabel('number of pixels')
if save_to_file:
p = PathStr(foldername).join(filename).setFiletype(filetype)
pyplot.savefig(p)
with open(PathStr(foldername).join('%s_params.csv' % filename),
'w') as f:
f.write('#x, #y, #fit\n')
for n, (x, y, ys) in enumerate(zip(xvals, yvals)):
fstr = ', '.join(str(f[n]) for f in fit)
f.write('%s, %s, %s\n' % (x, y, fstr))
if show_plots:
pyplot.show()
def start(self):
'''
configure the server and check the
message-inbox every self.opts['refeshrate']
'''
self._files = PathStr(self.opts['folder']).listdir()
self.timer = QtCore.QTimer()
self.timer.timeout.connect(self.checkFolder)
self.timer.start(self.opts['refreshrate'])
def _docopyToNewFolder(self):
self.setEnabled(True)
f = self._tempF
m = self.selectionModel()
for index in m.selectedRows():
y = index.row()
path = self._path2(y)
self._root.join(path).copy(PathStr(f).join(path.basename()))
QtGui.QDesktopServices.openUrl(QtCore.QUrl(f))
self._downloadDone = self._downloadDone_backup
del self._tempF
del self._downloadDone_backup
def checkFolder(self):
'''
Check for new files/folders in self.opts['folder']
and import them into dataArtist
'''
fo = PathStr(self.opts['folder'])
o = self.opts['files only']
files = fo.listdir()
for f in files:
if f not in self._files:
ff = fo.join(f)
if not o or ff.isfile():
self.gui.addFilePath(ff)
self._files = files
def _getDockTitle(title, number, names):
'''
create a title for this display dock
names -> list instances of PathStr
'''
docktitle = '[%s] ' % number
if title:
docktitle += title
if len(names) > 1:
#if multiple files imported:
#FOLDER IN TITLE
dirname = PathStr(names[0]).dirname()
if len(dirname) > 20:
dirname = '~' + dirname[-20:]
docktitle += "%s files from %s" % (len(names), dirname)
elif names and names != [None]:
#FILENAME IN TITLE
name = PathStr(names[0]).basename()
if len(name) > 20:
name = name[:8] + '(...)' + name[-8:]
docktitle += name
return docktitle
def equalizeImage(img, save_path=None, name_additive='_eqHist'):
'''
Equalize the histogram (contrast) of an image
works with RGB/multi-channel images
and flat-arrays
@param img - image_path or np.array
@param save_path if given output images will be saved there
@param name_additive if given this additive will be appended to output images
@return output images if input images are numpy.arrays and no save_path is given
@return None elsewise
'''
if isinstance(img, string_types):
img = PathStr(img)
if not img.exists():
raise Exception("image path doesn't exist")
img_name = img.basename().replace('.', '%s.' % name_additive)
if save_path is None:
save_path = img.dirname()
img = cv2.imread(img)
if img.dtype != np.dtype('uint8'):
# openCV cannot work with float arrays or uint > 8bit
eqFn = _equalizeHistogram
else:
eqFn = cv2.equalizeHist
if len(img.shape) == 3: # multi channel img like rgb
for i in range(img.shape[2]):
img[:, :, i] = eqFn(img[:, :, i])
else: # grey scale image
img = eqFn(img)
if save_path:
img_name = PathStr(save_path).join(img_name)
cv2.imwrite(img_name, img)
return img
def __call__(self, path, prevFn=None, nextFn=None):
ftype = PathStr(path).filetype()
V = None
if ftype != 'svg':
if ftype in QtGui.QImageReader.supportedImageFormats():
V = InlineView_image
elif ftype == 'csv':
V = _CSVviewer
elif ftype == 'txt':
V = _Txtviewer
if V is None:
return os.startfile(path)
self._prep(V, path, prevFn, nextFn)
return V
def valsFromPath(self):
colDate = MATRIX_HEADER.index('Date')
for row in range(self.rowCount()):
if self._allowModelToModifyCells:
path = PathStr(self.item(row, 0).text())
_success, entries = self.drawWidget.model(path)
for col, e in enumerate(entries):
col += 1
# if e == '':
# item = self.item(row, col)
# if hasattr(item, 'metaText'):
# e = self.item(row, col).metaText
if e != '':
self.setCell(row, col, str(e))
# add date from file date is not already given:
if not self.itemText(row, colDate):
self.setCell(row, colDate, datetime.fromtimestamp(
path.date()).strftime('%Y/%m/%d %H:%M:%S'))
def html2data(html):
'''
extract either tables or images from html code
'''
paths = []
data = []
doc = lxml.html.fromstring(html)
#images in html
for img in doc.xpath('img'):
#get the scr-path of the image:
imgsrc = img.get('src')
fname = PathStr(imgsrc).basename()
fpath = TMP_IMG_DIR.join(fname)
#download the image in a temporary folder:
urllib.urlretrieve(imgsrc, fpath)
paths.append(fpath)
#tables
table = _html2PyTable(doc)
if table:
data.append(table)
return paths, data
def _getFilePathsFromUrls(self, urls):
'''
return a list of all file paths in event.mimeData.urls()
'''
l = []
def _appendRecursive(path):
if path.isfile():
#file
l.append(path)
else:
for f in path:
#for all files in folder
_appendRecursive(path.join(f))
# one or more files/folders are dropped
for url in urls:
if url.isLocalFile():
path = PathStr(url.toLocalFile().toLocal8Bit().data())
if path.exists():
_appendRecursive(path)
return l
def model(self, path):
'''
depending on adjusted label positions,
split given path into MATRIX row
'''
names = path.splitNames()[-self.N_LAST_FOLDERS:]
names[-1] = PathStr(names[-1]).rmFileType()
out = [''] * (len(MATRIX_HEADER) - 1)
success = True
for i, n in enumerate(names):
item = self._lGrid.itemAtPosition(1, (2 * i) + 1)
if item:
txt = item.widget().text()
try:
fn = CAT_FUNCTIONS[txt]
fn(out, n)
except KeyError:
toRow(out, parsePath(n, txt))
except IndexError:
pass
return success, out
def _getFilePathsFromUrls(self, urls):
'''
return a list of all file paths in event.mimeData.urls()
'''
limg, lagenda = [], []
def _appendRecursive(path):
if path.isfile():
if path.filetype() in IMG_FILETYPES:
limg.append(path)
elif path.filetype() == 'csv':
lagenda.append(path)
else:
for f in path:
# for all files in folder
_appendRecursive(path.join(f))
# one or more files/folders are dropped
for url in urls:
if url.isLocalFile():
path = PathStr(url.toLocalFile())
if path.exists():
_appendRecursive(path)
return limg, lagenda
mx = mn
img /= mx
img = exposure.equalize_hist(img, nbins=nBins)
img *= mx
if intType:
img = img.astype(intType)
return img
if __name__ == '__main__':
import sys
import pylab as plt
import imgProcessor
from imgProcessor.imgIO import imread
img = imread(PathStr(imgProcessor.__file__).dirname().join(
'media', 'electroluminescence', 'EL_module_orig.PNG'))
eq = equalizeImage(img.copy())
if 'no_window' not in sys.argv:
plt.figure('original')
plt.imshow(img)
plt.figure('equalised histogram')
plt.imshow(eq)
plt.show()
'''
Quantitative ElectroLuminescence Analysis
'''
from fancytools.os.PathStr import PathStr
name = 'QELA'
__version__ = '-' # time stamp, set by server during packaging
__author__ = 'Karl Bedrich'
__email__ = '*****@*****.**'
__license__ = 'GPLv3'
# MEDIA_PATH = PathStr.getcwd().join('client', 'media') #only works if
# executed from main dir
MEDIA_PATH = PathStr(__file__).dirname().join(
'media') # TODO: works in FROZEN?
ICON = MEDIA_PATH.join('logo.svg')
PATH = PathStr.home().mkdir(".%s" % name)
def getBackgroundLevel(img):
#seems to be best one according of no-ref bg comparison
#as done for SNR article in BEDRICH2016 JPV
return median_filter(img[10:-10:10,10:-10:10],7).min()
if __name__ == '__main__':
import sys
from fancytools.os.PathStr import PathStr
import imgProcessor
from imgProcessor.imgIO import imread
import pylab as plt
p = PathStr(imgProcessor.__file__).dirname().join(
'media', 'electroluminescence')
img = imread(p.join('EL_cell_cracked.png'), 'gray')
snr = SNR(img)
if 'no_window' not in sys.argv:
plt.figure('image')
plt.imshow(img)
plt.colorbar()
plt.figure('SNR')
plt.imshow(snr)
plt.colorbar()
plt.show()
# self.camOpts.addItem(c['name'])
# self.camOpts.setCurrentIndex(self.camOpts.count() - 1)
if __name__ == '__main__':
import sys
from fancytools.os.PathStr import PathStr
#######################
# temporary fix: app crack doesnt through exception
# https://stackoverflow.com/questions/38020020/pyqt5-app-exits-on-error-where-pyqt4-app-would-not
sys.excepthook = lambda t, v, b: sys.__excepthook__(t, v, b)
#######################
app = QtWidgets.QApplication([])
w = TabCheck()
imgs = PathStr(
r'D:\Measurements\TrinaPID_EL\EL\source\02ND ROUND\8A').files()
# w.addImgs(imgs)
# w.buildTree('''ID1 {"grid":[6,10], "sublines":[[],[]]}
# meas1 {"vertices":[[[0, 0], [2, 0], [1, 1], [0, 1]]], "validated":0}
# cur1
# cur2
# mea2 {"vertices":[[[0, 0], [2, 0], [1, 1], [0, 1]]], "validated":0}
# cur1
# cur2
# ID2
# ID3
# ''')
# childItem = QtWidgets.QTreeWidgetItem(w.list.item(0))
# w.list.item(0).insertChild(0, 'ss')
