def RunShapeFileImportTool():
"""
<Script>
<Author>admin</Author>
<Description>Please enter script description here</Description>
</Script>
"""
# Get all the files in the directory
directory = r"C:\temp\Del_Shape" #directory with shape files
FileList = Directory.GetFiles(directory)
DB_folder = '/xx' #folder to import shape files to
for file in FileList:
fullPath = Path.Combine(directory, file)
if Path.GetExtension(fullPath) == '.shp':
featureClassName = '/' + Path.GetFileNameWithoutExtension(
fullPath) #filenameWithoutExtension
inputItems = gisMgr.FeatureClassGroupList.Get(DB_folder)
if inputItems == None:
inputItems = gisMgr.FeatureClassGroupList.CreateNew(DB_folder)
coordinateSystem = gisMgr.DefaultCoordinateSystem
ShapeFileImportTool(inputItems, coordinateSystem, featureClassName,
fullPath)
def GetCurrentSessionIds(folderPath):
ids = []
file_list = glob.glob(folderPath + '\\*' + '.txt')
for f in file_list:
ids.append(
AdjustSessionIdFileNameBack(Path.GetFileNameWithoutExtension(f)))
return ids
def run_postprocessing(image, parameters={}, func='topography'):
"""Example template to add post-processing functions.
:param image: Image to be processed
:type image: ZenImage
:param parameters: Dictionary with processing parameters for function, defaults to {}
:type parameters: dict, optional
:param func: Function name, defaults to 'topography'
:type func: str, optional
:return: image or processed image
:rtype: ZenImage
"""
if func == 'topography':
noise_low = parameters['noise_low']
noise_high = parameters['noise_high']
outputfolder = parameters['outputfolder']
ext = parameters['extension']
# converting to topo, with defined FZ noisecut
# in filter settings: 0-255 means no filter, 1-254 means cut one gray scale from top and from bottom
imgtop = Zen.Processing.Transformation.Topography.CreateTopography(
image, noise_low, noise_high)
# saving file to the directory
topo_filepath = Path.Combine(
outputfolder,
Path.GetFileNameWithoutExtension(image.FileName) + ext)
Zen.Processing.Utilities.ExportHeightmapFromTopography(
imgtop, topo_filepath)
print('Exported to : ', topo_filepath)
imgtop.Close()
return image
def ExecuteFile(self, filename, globalVar=None):
moduleEO = self.CreateScope()
self.dbgmodule = moduleEO
self.ExecuteFileInScope(filename, moduleEO)
globalVar = globalVar or Path.GetFileNameWithoutExtension(filename)
runtime.DynamicObjectHelpers.SetMember(self.Globals, globalVar,
moduleEO)
return moduleEO
def SaveCoverAsImage(books): for book in books: bookFileInfo = FileInfo(book.FilePath) bookNameWithoutExt = Path.GetFileNameWithoutExtension(book.FilePath); dirName = bookFileInfo.DirectoryName destinationFilePath = dirName + "\\" + bookNameWithoutExt + '.jpg' pageImage = ComicRack.App.GetComicPage(book, book.FrontCoverPageIndex) pageImage.Save(destinationFilePath, ImageFormat.Jpeg)
def run(self, Mml2vgmInfo, index):
#設定値の読み込み
Mml2vgmInfo.loadSetting()
#初回のみ(設定値が無いときのみ)git.exeの場所をユーザーに問い合わせ、設定値として保存する
gt = Mml2vgmInfo.getSettingValue("soxpath")
if gt is None:
gt = Mml2vgmInfo.fileSelect(
"sox.exeを選択してください(この選択内容は設定値として保存され次回からの問い合わせはありません)")
if not Mml2vgmInfo.confirm("sox.exeの場所は以下でよろしいですか\r\n" + gt):
return None
Mml2vgmInfo.setSettingValue("soxpath", gt)
Mml2vgmInfo.saveSetting()
#念のため
if gt is None or gt == "":
Mml2vgmInfo.msg("sox.exeを指定してください")
return None
#ファイル情報の整理
for fnf in Mml2vgmInfo.fileNamesFull:
ext = Path.GetExtension(fnf)
bas = Path.GetFileNameWithoutExtension(fnf)
wp = Path.GetDirectoryName(fnf)
Directory.SetCurrentDirectory(wp)
si = ScriptInfo()
# 引数を組み立てる
if index == 0:
args = "--i \"" + bas + ext + "\""
elif index == 1:
# -b 8bit
# -c 1 mono
# -r 14k rate 14KHz
args = bas + ext + " -b 8 -r 8k -c 1 " + bas + "_8k" + ext
elif index == 2:
args = bas + ext + " -r 14k -e signed-integer -c 1 " + bas + "_14k" + ext
elif index == 3:
args = bas + ext + " -r 16k -e signed-integer -c 1 " + bas + "_16k" + ext
elif index == 4:
args = bas + ext + " -r 18500 -e signed-integer -c 1 " + bas + "_18500" + ext
ret = Mml2vgmInfo.runCommand(gt, args, True)
if ret != "":
Mml2vgmInfo.msg(ret)
else:
if index != 0:
Mml2vgmInfo.msg("success")
Mml2vgmInfo.refreshFolderTreeView()
return si
def run(self, Mml2vgmInfo, index):
#設定値の読み込み
Mml2vgmInfo.loadSetting()
#初回のみ(設定値が無いときのみ)mucom88.exeの場所をユーザーに問い合わせ、設定値として保存する
mc = Mml2vgmInfo.getSettingValue("mucom88path")
if mc is None:
mc = Mml2vgmInfo.fileSelect(
"mucom88.exeを選択してください(この選択内容は設定値として保存され次回からの問い合わせはありません)")
if not Mml2vgmInfo.confirm("mucom88.exeの場所は以下でよろしいですか\r\n" + mc):
return None
Mml2vgmInfo.setSettingValue("mucom88path", mc)
Mml2vgmInfo.saveSetting()
#念のため
if mc is None or mc == "":
Mml2vgmInfo.msg("mucom88.exeを指定してください")
return None
#ファイル選択
muc = Mml2vgmInfo.fileSelect("mucファイルの選択")
if muc is None:
return None
#ファイル情報の整理
#Mml2vgmInfo.msgLogWindow(muc)
wp = Path.GetDirectoryName(muc)
#Mml2vgmInfo.msgLogWindow(wp)
Directory.SetCurrentDirectory(wp)
#mucom88.exeでコンパイルを行いmubファイルを生成する
args = "-c " + muc
Mml2vgmInfo.runCommand(mc, args, True)
#mubファイルが出来たかチェック(mucom88.exeはコンパイルが成功するとmucom88.mubというファイルができる)
mm = Path.Combine(wp, "mucom88.mub")
#Mml2vgmInfo.msgLogWindow(mm)
if not File.Exists(mm):
return None
#mucom88.mubを本来のファイル名にリネーム
mub = Path.Combine(wp, Path.GetFileNameWithoutExtension(muc) + ".mub")
#Mml2vgmInfo.msgLogWindow(mub)
File.Delete(mub)
File.Move(mm, mub)
#mucom88.exeで演奏を開始
Mml2vgmInfo.runCommand(mc, mub, False)
#戻り値を生成(何もしないけど念のため)
si = ScriptInfo()
si.responseMessage = ""
return si
def run(self, Mml2vgmInfo, index):
#設定値の読み込み
Mml2vgmInfo.loadSetting()
#初回のみ(設定値が無いときのみ)sox.exeの場所をユーザーに問い合わせ、設定値として保存する
gt = Mml2vgmInfo.getSettingValue("soxpath")
if gt is None:
gt = Mml2vgmInfo.fileSelect(
"sox.exeを選択してください(この選択内容は設定値として保存され次回からの問い合わせはありません)")
if not Mml2vgmInfo.confirm("sox.exeの場所は以下でよろしいですか\r\n" + gt):
return None
Mml2vgmInfo.setSettingValue("soxpath", gt)
Mml2vgmInfo.saveSetting()
#念のため
if gt is None or gt == "":
Mml2vgmInfo.msg("sox.exeを指定してください")
return None
#ファイル情報の整理
for fnf in Mml2vgmInfo.fileNamesFull:
ext = Path.GetExtension(fnf)
bas = Path.GetFileNameWithoutExtension(fnf)
wp = Path.GetDirectoryName(fnf)
Directory.SetCurrentDirectory(wp)
si = ScriptInfo()
argList = [
"--i \"{0}{1}\"",
"\"{0}{1}\" -r 8000 -b 8 -c 1 \"{0}_8k{1}\"",
"\"{0}{1}\" -r 14000 -b 8 -c 1 \"{0}_14k{1}\"",
"\"{0}{1}\" -r 16000 -b 8 -c 1 \"{0}_16k{1}\"",
"\"{0}{1}\" -r 18500 -b 8 -c 1 \"{0}_18500{1}\"",
"\"{0}{1}\" -b 16 -r 14000 -e signed-integer -c 1 \"{0}_16b_14k{1}\"",
"\"{0}{1}\" -b 16 -r 16000 -e signed-integer -c 1 \"{0}_16b_16k{1}\"",
"\"{0}{1}\" -b 16 -r 18500 -e signed-integer -c 1 \"{0}_16b_18500{1}\"",
"\"{0}{1}\" -n trim 0 1.5 noiseprof \"{0}.noise-profile\"",
"\"{0}{1}\" \"{0}_cleaned{1}\" noisered \"{0}.noise-profile\" 0.2 "
]
args = argList[index].format(bas, ext)
ret = Mml2vgmInfo.runCommand(gt, args, True)
if ret != "":
Mml2vgmInfo.msg(ret)
else:
if index != 0:
Mml2vgmInfo.msg("success")
Mml2vgmInfo.refreshFolderTreeView()
return si
def DumpPlainTextLogFile():
plainTextLogFilePath = None
logFilePath = GetLogFilePath()
if not str.IsNullOrWhiteSpace(logFilePath):
plainTextLogFilePath = Path.Combine(
Path.GetDirectoryName(logFilePath),
Path.GetFileNameWithoutExtension(logFilePath) + ".txt")
try:
File.WriteAllLines(plainTextLogFilePath,
LogFile.ReadLinesAsPlainText(logFilePath))
except Exception, e:
plainTextLogFilePath = None
def FileComboBox_SelectionChanged(self, sender, e):
self.clear_plot()
if self.FileComboBox.SelectedIndex != -1:
comboIndex = self.FileComboBox.SelectedIndex
file_name = self.file_names[comboIndex]
data = parse_file(file_name)
stem = Path.GetFileNameWithoutExtension(file_name)
fig = self.generate_plot(
x=data['Stage_StageReadings_StagePasteMins1'],
y=data['Stage_StageReadings_StagePasteDive1'],
title=stem,
)
self.set_plot(fig)
def convert_files(doc_path):
directory = DirectoryInfo(doc_path)
files = directory.GetFiles("*.doc")
for file_info in files:
text = doc_to_text(Path.Combine(doc_path, file_info.Name))
stream_writer = File.CreateText(
Path.GetFileNameWithoutExtension(file_info.Name) + ".txt")
stream_writer.Write(text)
stream_writer.Close()
return
def main():
if len(sys.argv) != 2:
print "Usage: ipy run_compiled.py <testfile.py>"
sys.exit(-1)
testName = sys.argv[1]
print "Compiling ", testName ,"..."
clr.CompileModules("compiledTest.dll", testName)
File.Move(testName, testName+".bak")
try:
print "Running test from compiled binary..."
clr.AddReference("compiledTest")
__import__(Path.GetFileNameWithoutExtension(testName))
finally:
File.Move(testName+".bak" , testName)
def OptimizeAllIFCFilesinFolder(directoryPath):
returnvalue = res.Result()
# check if ifc optimizer is installed:
if(cp.FileExist(solibriInstallPath_)):
returnvalue.message = 'Solibri IFC optimizer is installed.'
ifcFiles = cp.GetFiles(directoryPath, '.ifc')
filesToDelete = []
filesToRename = []
if(len(ifcFiles) > 0):
returnvalue.AppendMessage('found ifc files: ' + str(len(ifcFiles)))
for ifcFile in ifcFiles:
s = subprocess.check_call([r'C:\Program Files\Solibri\IFCOptimizer\Solibri IFC Optimizer.exe', '-in=' + ifcFile, '-out=' + directoryPath, '-ifc', '-force'])
# check what came back
if (s == 0):
#all went ok:
returnvalue.AppendMessage('Optimized file: '+str(ifcFile))
filesToDelete.append(ifcFile) # full file path
# get the rename information
# contains old and new file name
rename = []
p = cp.GetFolderPathFromFile(ifcFile)
if(p != ''):
newFilePath = str(p)+'\\'+ str(Path.GetFileNameWithoutExtension(ifcFile))+'_optimized.ifc'
rename.append(newFilePath)
rename.append(ifcFile)
filesToRename.append(rename)
else:
# something went wrong
returnvalue.UpdateSep(False, 'Failed to optimize file: '+ str(ifcFile))
# clean up
for fileToDelete in filesToDelete:
statusDelete = cp.FileDelete(fileToDelete)
if(statusDelete):
returnvalue.AppendMessage('Deleted original file: ' + str(fileToDelete))
else:
returnvalue.UpdateSep(False,'Failed to delete original file: '+ str(fileToDelete))
for fileToRename in filesToRename:
statusRename = cp.RenameFile(fileToRename[0], fileToRename[1])
if(statusRename):
returnvalue.AppendMessage('Renamed original file: ' + str(fileToRename[0]) + ' to: ' + str(fileToRename[1]))
else:
returnvalue.UpdateSep(False,'Failed to rename original file: '+ str(fileToRename[0]))
else:
returnvalue.AppendMessage('No IFC files found in directory: '+ str(directoryPath))
else:
returnvalue.UpdateSep(False, 'No IFC optimizer installed at: '+ str(solibriInstallPath_))
return returnvalue
def run_postprocessing(image, parameters={}, func='topography'):
if func == 'topography':
noise_low = parameters['noise_low']
noise_high = parameters['noise_high']
outputfolder = parameters['outputfolder']
ext = parameters['extension']
# converting to topo, with defined FZ noisecut
# in filter settings: 0-255 means no filter, 1-254 means cut one gray scale from top and from bottom
imgtop = Zen.Processing.Transformation.Topography.CreateTopography(image, noise_low, noise_high)
# saving file to the directory
topo_filepath = Path.Combine(outputfolder, Path.GetFileNameWithoutExtension(image.FileName) + ext)
Zen.Processing.Utilities.ExportHeightmapFromTopography(imgtop, topo_filepath)
print('Exported to : ', topo_filepath)
imgtop.Close()
return image
def OpenFileButton_Click(self, sender, e):
dlg = OpenFileDialog()
dlg.DefaultExt = ".txt"
dlg.Filter = "Text Files (*.txt)|*.txt"
dlg.Multiselect = True
if dlg.ShowDialog() == True:
self.file_names = dlg.FileNames
self.combo_clear()
self.log_clear()
self.log_append(
f'Successfully loaded {len(self.file_names)} stages:')
for file_name in self.file_names:
stem = Path.GetFileNameWithoutExtension(file_name)
self.log_append(stem)
self.FileComboBox.Items.Add(stem)
self.SaveXMLButton.IsEnabled = True
self.FileComboBox.IsEnabled = True
# load image in Zen
img = Zen.Application.LoadImage(czifile, False)
Zen.Application.Documents.Add(img)
metadata = jt.fill_metadata(img)
IMAGEJ = 'c:\\Fiji\\ImageJ-win64.exe'
IMAGEJDIR = Path.GetDirectoryName(IMAGEJ)
SCRIPT = 'c:\\Fiji\\scripts\\3d_analytics_fromZEN.py'
# define script parameters
params = {}
params['IMAGEJ'] = IMAGEJ
params['IMAGEJSCRIPT'] = SCRIPT
params['IMAGE'] = czifile
params['IMAGEDIR'] = Path.GetDirectoryName(czifile)
params['FILEWOEXT'] = Path.GetFileNameWithoutExtension(czifile)
params['HEADLESS'] = True
# define processing parameters
params['JSONPARAMSFILE'] = Path.Combine(params['IMAGEDIR'],
params['FILEWOEXT'] + '.json')
params['LABEL_CONNECT'] = 6
params['LABEL_COLORIZE'] = False
params['MINVOXSIZE'] = 1000
# define outputs
params['SAVEFORMAT'] = 'ome.tiff'
params['RESULTTABLE'] = ''
params['RESULTIMAGE'] = ''
# update dictionary
def GetRevitModelName(revitFilePath):
return Path.GetFileNameWithoutExtension(revitFilePath)
def onSignInClick(source, rea):
config = None
directory = Path.Combine(
Environment.GetFolderPath(
Environment.SpecialFolder.ApplicationData),
Assembly.GetEntryAssembly().GetName().Name)
backgroundBrush = None
textColor = SystemColors.ControlTextBrush
if Directory.Exists(directory):
fileName1 = Path.GetFileName(Assembly.GetEntryAssembly().Location)
for fileName2 in Directory.EnumerateFiles(directory, "*.config"):
if fileName1.Equals(
Path.GetFileNameWithoutExtension(fileName2)):
exeConfigurationFileMap = ExeConfigurationFileMap()
exeConfigurationFileMap.ExeConfigFilename = fileName2
config = ConfigurationManager.OpenMappedExeConfiguration(
exeConfigurationFileMap, ConfigurationUserLevel.None)
if config is None:
config = ConfigurationManager.OpenExeConfiguration(
ConfigurationUserLevel.None)
directory = None
if config.AppSettings.Settings["BackgroundImage"] is not None:
fileName = config.AppSettings.Settings[
"BackgroundImage"].Value if directory is None else Path.Combine(
directory,
config.AppSettings.Settings["BackgroundImage"].Value)
fs = None
bi = BitmapImage()
try:
fs = FileStream(fileName, FileMode.Open, FileAccess.Read,
FileShare.Read)
bi.BeginInit()
bi.StreamSource = fs
bi.CacheOption = BitmapCacheOption.OnLoad
bi.CreateOptions = BitmapCreateOptions.None
bi.EndInit()
finally:
if fs is not None:
fs.Close()
backgroundBrush = ImageBrush(bi)
backgroundBrush.TileMode = TileMode.Tile
backgroundBrush.ViewportUnits = BrushMappingMode.Absolute
backgroundBrush.Viewport = Rect(0, 0, bi.Width, bi.Height)
backgroundBrush.Stretch = Stretch.None
if backgroundBrush.CanFreeze:
backgroundBrush.Freeze()
if backgroundBrush is None and config.AppSettings.Settings[
"BackgroundColor"] is not None:
if config.AppSettings.Settings["BackgroundColor"].Value.Length > 0:
backgroundBrush = SolidColorBrush(
ColorConverter.ConvertFromString(
config.AppSettings.Settings["BackgroundColor"].Value))
if backgroundBrush.CanFreeze:
backgroundBrush.Freeze()
if config.AppSettings.Settings["TextColor"] is not None:
if config.AppSettings.Settings["TextColor"].Value.Length > 0:
textColor = ColorConverter.ConvertFromString(
config.AppSettings.Settings["TextColor"].Value)
textBrush = SolidColorBrush(textColor)
if textBrush.CanFreeze:
textBrush.Freeze()
window = Window()
def onClick(source, args):
global username, password
if not String.IsNullOrEmpty(
usernameTextBox.Text) and not String.IsNullOrEmpty(
passwordBox.Password):
username = usernameTextBox.Text
password = passwordBox.Password
def onSave():
try:
fs = None
sr = None
sw = None
try:
fs = FileStream(__file__, FileMode.Open,
FileAccess.ReadWrite,
FileShare.Read)
encoding = UTF8Encoding(False)
sr = StreamReader(fs, encoding, True)
lines = Regex.Replace(
Regex.Replace(
sr.ReadToEnd(), "username\\s*=\\s*\"\"",
String.Format("username = \"{0}\"",
username),
RegexOptions.CultureInvariant),
"password\\s*=\\s*\"\"",
String.Format("password = \"{0}\"", password),
RegexOptions.CultureInvariant)
fs.SetLength(0)
sw = StreamWriter(fs, encoding)
sw.Write(lines)
finally:
if sw is not None:
sw.Close()
if sr is not None:
sr.Close()
if fs is not None:
fs.Close()
except Exception, e:
Trace.WriteLine(e.clsException.Message)
Trace.WriteLine(e.clsException.StackTrace)
def onCompleted(task):
global menuItem
for window in Application.Current.Windows:
if window is Application.Current.MainWindow and window.ContextMenu is not None:
if window.ContextMenu.Items.Contains(menuItem):
window.ContextMenu.Items.Remove(menuItem)
window.ContextMenu.Opened -= onOpened
if window.ContextMenu.Items[10].GetType(
).IsInstanceOfType(window.ContextMenu.Items[
window.ContextMenu.Items.Count - 4]):
window.ContextMenu.Items.RemoveAt(10)
menuItem = None
Task.Factory.StartNew(
onSave, TaskCreationOptions.LongRunning).ContinueWith(
onCompleted,
TaskScheduler.FromCurrentSynchronizationContext())
window.Close()
if surface_result:
surface = 'True'
elif not surface_result:
surface = 'False'
# define the actual CZI file to be analyzed
czifile = CZIdict[cziname]
czifile_cmd = '"' + CZIdict[cziname] + '"'
params = czifile_cmd + ' ' + writecsv + ' ' + separator + ' ' + save + ' ' + saveformat_result + ' ' + surface
print 'CZI file to be used: ', czifile
print 'Parameter : ', params
# when option to save the figure was set
if save_result:
savename = Path.GetFileNameWithoutExtension(
czifile) + '_planetable_XYZ-Pos.' + saveformat_result
savename_full = Path.Combine(Path.GetDirectoryName(czifile), savename)
print 'Savename: ', savename_full
# delete older version of the figure if existing
if File.Exists(savename_full):
File.Delete(savename_full)
print 'Deleted older figure: ', savename_full
# start the data display script as an external application
app = Process()
app.StartInfo.FileName = SCRIPT
app.StartInfo.Arguments = params
app.Start()
# waits until the python figure was closed
app.WaitForExit()
# specify image
image_to_analyze = r'c:\Data\Nanoparticles.tif'
# define the image analysis setting
iasfilename = r'c:\Users\XYZ\Documents\Carl Zeiss\ZEN\Documents\Image Analysis Settings\Nanoparticle Segmentation ZEN25.czias'
# define the external plot script or tool
pythonexe = r'C:\Anaconda3\python.exe'
script = r'c:\Data\External_Python_Scripts_for_OAD\RMI_plot_nanoparticles.py'
# load imnage
image = Zen.Application.LoadImage(image_to_analyze)
Zen.Application.Documents.Add(image)
outputpath = Path.GetDirectoryName(image_to_analyze)
resultname = Path.GetFileNameWithoutExtension(image.Name)
# loead CZIAS image analysis setting
ias = ZenImageAnalysisSetting()
ias.Load(iasfilename)
classnames = ias.GetRegionClassNames()
if analyze_inplace:
Zen.Analyzing.Analyze(image, ias)
# run the image analyis pipeline and directly create a table
all_tables = Zen.Analyzing.AnalyzeToTable(image, ias)
for class_table in all_tables:
if show_tables:
print 'Confidence Threshold Value : ', conf_th
print 'Add Segmented Image to Original : ', addseg2orig
print 'Adapt PixelType of Segmented Image : ', adaptpx
print '-----------------------------------------------------------------------------'
print 'Segmenting ...'
# extract select channel from active image
substr = 'C(' + str(chdict[channelname]) + ')'
image = Zen.Processing.Utilities.CreateSubset(activeimage, substr, False)
# do the pixel classification for the current image
seg = classify(image,
modelname,
use_confidence=use_conf,
confidence_threshold=conf_th,
format=segmentationformat,
extractclass=extract,
addseg=False,
classid=extract_id + 1,
adapt_pixeltype=adaptpx)
if addseg2orig:
# add segmentation result to the original image
orig_seg = Zen.Processing.Utilities.AddChannels(activeimage, seg)
Zen.Application.Documents.Add(orig_seg)
seg_name = Path.GetFileNameWithoutExtension(
activeimagefilename) + '_seg' + Path.GetExtension(activeimagefilename)
orig_seg.Name = seg_name
print 'Done.'
if verbose:
for i in info:
print i.Key, ':\t ', i.Value
# get additional metainformation
metadata = getMetaDataExtra(activeimage, usecounter, fullwellinfo=fwinfo)
if verbose:
for k, v in metadata.iteritems():
print k, ':\t', v
# concatenate the two python dictionaries
metadata.update(info)
# Create new table with 2 col with name Key and Value
table1 = ZenTable('MetaData - ' + Path.GetFileNameWithoutExtension(cziname))
table1.Columns.Add('Name',str)
table1.Columns.Add('Value',str)
# fill the table from the dictionary
r = 0
for k, v in metadata.iteritems():
table1.Rows.Add()
table1.SetValue(r, 0, k)
table1.SetValue(r, 1, v)
r = r + 1
# sort the table
table1_sorted = SortZenTable(table1, 'Name')
Zen.Application.Documents.Add(table1_sorted)
if not File.Exists(script):
message = 'Plot Script not found.'
print(message)
raise SystemExit
if File.Exists(script):
message = 'Plot Script found.'
print(message)
# load image and add it to ZEN and get the image path
image_to_analyze = r'c:\Testdata\Translocation_comb_96_5ms.czi'
image = Zen.Application.LoadImage(image_to_analyze)
Zen.Application.Documents.Add(image)
outputpath = Path.GetDirectoryName(image_to_analyze)
resultname = Path.GetFileNameWithoutExtension(image.Name)
# define the image analysis setting and run the image analysis on the active image
iasfilename = r'c:\Image Analysis Settings\Translocation_ZEN2.6.czias'
ias = ZenImageAnalysisSetting()
ias.Load(iasfilename)
Zen.Analyzing.Analyze(image, ias)
"""
# Create data list with results for all regions (e.g. all nuclei)
table_all = Zen.Analyzing.CreateRegionsTable(image)
Zen.Application.Documents.Add(table_all)
# Create data list with results for each region (e.g. every single nucleus)
table_single = Zen.Analyzing.CreateRegionTable(image)
Zen.Application.Documents.Add(table_single)
"""
from System.Diagnostics import Process from System.IO import File, Path, Directory # clear output Zen.Application.Documents.RemoveAll(False) Zen.Application.MacroEditor.ClearMessages() # define output folder outputpath = r'c:\Output' # initialize Zen experiment and run it experiment_filename = r'ML_96_Wellplate_Castor.czexp' exp = ZenExperiment() exp.Load(experiment_filename) image2analyze = Zen.Acquisition.Execute(exp) # save the image savename = Path.GetFileNameWithoutExtension(experiment_filename) + '.czi' image2analyze.Save(Path.Combine(outputpath, savename)) # define the image analysis setting and run the image analysis on the active image iafilename = r'c:\Users\M1SRH\Documents\Carl Zeiss\ZEN\Documents\Image Analysis Settings\Count_Cells_DAPI_96well.czias' ias = ZenImageAnalysisSetting() ias.Load(iafilename) Zen.Analyzing.Analyze(image2analyze, ias) # Create data list with results for all regions (e.g. all nuclei) table_all = Zen.Analyzing.CreateRegionsTable(image2analyze) Zen.Application.Documents.Add(table_all) # Create data list with results for each region (e.g. every single nucleus) table_single = Zen.Analyzing.CreateRegionTable(image2analyze) Zen.Application.Documents.Add(table_single)
def renderArgument(self):
renderEngines = {
"V-Ray": "0",
"V-Ray RT": "1",
u"V-Ray RT(OpenCL)": "3",
u"V-Ray RT(CUDA)": "5"
}
sRGBOptions = ["On", "Off"]
displayWindow = self.GetBooleanPluginInfoEntryWithDefault(
"DisplayVFB", False)
autoclose = self.GetBooleanPluginInfoEntryWithDefault(
"AutocloseVFB", True)
displaySRGB = self.GetPluginInfoEntryWithDefault("DisplaySRGB", "On")
# Get the frame information.
startFrame = self.GetStartFrame()
endFrame = self.GetEndFrame()
singleRegionJob = self.IsTileJob()
singleRegionFrame = str(self.GetStartFrame())
singleRegionIndex = self.GetCurrentTaskId()
separateFilesPerFrame = self.GetBooleanPluginInfoEntryWithDefault(
"SeparateFilesPerFrame", False)
regionRendering = self.GetBooleanPluginInfoEntryWithDefault(
"RegionRendering", False)
rtEngine = self.GetPluginInfoEntryWithDefault("VRayEngine", "V-Ray")
rtTimeout = self.GetFloatPluginInfoEntryWithDefault("RTTimeout", 0.00)
rtNoise = self.GetFloatPluginInfoEntryWithDefault("RTNoise", 0.001)
rtSampleLevel = self.GetIntegerPluginInfoEntryWithDefault(
"RTSamples", 0)
# Can't allow it to be interactive or display the image because that would hang the slave
renderarguments = " -scenefile=\"" + self.tempSceneFilename + "\" -interactive=0"
if not displayWindow:
renderarguments += " -display=0" # Default value is 1
else:
if autoclose:
renderarguments += " -autoclose=1" # Default value is 0
renderarguments += " -displaySRGB=%s" % (
sRGBOptions.index(displaySRGB) + 1)
renderarguments += " -rtEngine=%s" % renderEngines[rtEngine.strip()]
if not rtEngine == "V-Ray":
renderarguments += " -rtTimeOut=%s -rtNoise=%s -rtSampleLevel=%s" % (
rtTimeout, rtNoise, rtSampleLevel)
renderarguments += " -frames=" + str(startFrame)
if endFrame > startFrame:
renderarguments += "-" + str(endFrame)
# Set the output path.
outputFile = self.GetPluginInfoEntryWithDefault("OutputFilename",
"").strip()
if outputFile != "":
outputFile = RepositoryUtils.CheckPathMapping(outputFile)
outputFile = PathUtils.ToPlatformIndependentPath(outputFile)
if regionRendering:
outputPath = Path.GetDirectoryName(outputFile)
outputFileName = Path.GetFileNameWithoutExtension(outputFile)
outputExtension = Path.GetExtension(outputFile)
if singleRegionJob:
outputFile = os.path.join(
outputPath, ("_tile%s_" % singleRegionIndex) +
outputFileName + outputExtension)
else:
currTile = self.GetIntegerPluginInfoEntryWithDefault(
"CurrentTile", 1)
outputFile = os.path.join(outputPath,
("_tile%d_" % currTile) +
outputFileName + outputExtension)
renderarguments += " -imgFile=\"" + outputFile + "\""
# Now set the rest of the options.
renderarguments += " -numThreads=" + str(self.GetThreadCount())
width = self.GetIntegerPluginInfoEntryWithDefault("Width", 0)
if width > 0:
renderarguments += " -imgWidth=" + str(width)
height = self.GetIntegerPluginInfoEntryWithDefault("Height", 0)
if height > 0:
renderarguments += " -imgHeight=" + str(height)
if regionRendering:
regionNumString = ""
if singleRegionJob:
regionNumString = str(singleRegionIndex)
#Coordinates In Pixels will always be true when using the common tilerendering code.
if self.GetBooleanPluginInfoEntryWithDefault(
"CoordinatesInPixels", False):
#With the coordinates already being in pixels we do not need to modify the coordinates.
xStart = self.GetIntegerPluginInfoEntryWithDefault(
"RegionXStart" + regionNumString, 0)
xEnd = self.GetIntegerPluginInfoEntryWithDefault(
"RegionXEnd" + regionNumString, 0)
yStart = self.GetIntegerPluginInfoEntryWithDefault(
"RegionYStart" + regionNumString, 0)
yEnd = self.GetIntegerPluginInfoEntryWithDefault(
"RegionYEnd" + regionNumString, 0)
else:
self.LogWarning(
"Using deprecated coordinate system. Please submit new jobs to use the new coordinates system."
)
xStart = round(
self.GetFloatPluginInfoEntryWithDefault(
"RegionXStart" + regionNumString, 0) * width)
xEnd = round(
self.GetFloatPluginInfoEntryWithDefault(
"RegionXEnd" + regionNumString, 0) * width)
yStart = round(
self.GetFloatPluginInfoEntryWithDefault(
"RegionYStart" + regionNumString, 0) * height)
yEnd = round(
self.GetFloatPluginInfoEntryWithDefault(
"RegionYEnd" + regionNumString, 0) * height)
renderarguments += " -region=%d;%d;%d;%d" % (xStart, yStart, xEnd,
yEnd)
disableProgressColor = self.GetBooleanConfigEntryWithDefault(
"DisableProgressColor", False)
if disableProgressColor:
renderarguments += " -DisableProgressColor=0"
renderarguments += " " + self.GetPluginInfoEntryWithDefault(
"CommandLineOptions", "")
yetiSearchPaths = []
searchPathIndex = 0
while True:
searchPath = self.GetPluginInfoEntryWithDefault(
"YetiSearchPath" + str(searchPathIndex),
"").replace("\\", "/")
if not searchPath:
break
yetiSearchPaths.append(
RepositoryUtils.CheckPathMapping(searchPath))
searchPathIndex += 1
if len(yetiSearchPaths) > 0:
oldSearchPath = os.environ.get("PG_IMAGE_PATH")
if oldSearchPath:
yetiSearchPaths.append(oldSearchPath)
yetiSepChar = ":"
if SystemUtils.IsRunningOnWindows():
yetiSepChar = ";"
self.SetProcessEnvironmentVariable(
"PG_IMAGE_PATH", yetiSepChar.join(yetiSearchPaths))
return renderarguments
def import_animation(target):
brres = BrawlAPI.RootNode
# verify model exists
model_wrapper = None
model = None
for mdl in BrawlAPI.NodeWrapperListOfType[MDL0Wrapper]():
if mdl.Resource.Name == "course":
model_wrapper = mdl
model = mdl.Resource
# verify material exists
material = None
for mat in model.FindChildrenByType("/", ResourceType.MDL0Material):
if mat.Name == target:
material = mat
if material == None or model_wrapper == None or model == None:
return
################
### Clean Up ###
################
for reference in material.GetChildrenRecursive():
# delete old textures
for texture in BrawlAPI.NodeListOfType[TEX0Node]():
if texture.Name == reference.Name:
texture.Remove(True)
# delete old mdl0 texture references
for mdl0_tex in BrawlAPI.NodeListOfType[MDL0TextureNode]():
if mdl0_tex.Name == reference.Name:
mdl0_tex.Remove()
# delete old animation
for srt in BrawlAPI.NodeListOfType[SRT0Node]():
for srt_subnode in srt.Children:
if srt_subnode.Name == material.Name:
srt.Remove()
#################
### Importing ###
#################
for filename in Directory.GetFiles(preset_path):
# import textures
if filename.endswith(".tex0"):
node = NodeFactory.FromFile(None, filename)
brres.GetOrCreateFolder[TEX0Node]().AddChild(node)
# import material
if filename.endswith(".mdl0mat"):
material.Replace(filename)
material.Name = Path.GetFileNameWithoutExtension(filename)
# import shader and set material shader
if filename.endswith(".mdl0shade"):
# replace shader if only in use by target
if len(material.ShaderNode.Materials) == 1:
material.ShaderNode.Replace(filename)
# otherwise make a new shader
else:
shader = model_wrapper.NewShader()
shader.Replace(filename)
material.ShaderNode = shader
# import animation and rename material
if filename.endswith(".srt0"):
node = NodeFactory.FromFile(None, filename)
brres.GetOrCreateFolder[SRT0Node]().AddChild(node)
# show output window
output.Show()
output.WriteLine('Setting temperature to ' + str(temp) + '[*C]')
output.WriteLine('Setting humidity to ' + str(hum) + '[%]')
output.WriteLine('Setting pressure to ' + str(pres) + '[hPa]')
# channel var
ch = 0
# iterate over all folders
for file in files:
ch = ch + 1
# get file paths
folder = Path.GetDirectoryName(file)
name = Path.GetFileNameWithoutExtension(file)
ext = Path.GetExtension(file)
newname = folder + '\\' + 'edited_' + str(ch) + '_' + name + ext
wave = waves.LoadWave(file)
wave.AudioFile.Temperature = temp
wave.AudioFile.Humidity = hum
wave.AudioFile.Pressure = pres
wave.AudioFile.ReceiverNo = ch
wave.SaveAs(newname)
output.WriteLine('Saving as: ' + newname + ' - ok')
wave.Close() # make sure to close the file, otherwise you'll run out of memory
output.WriteLine('That\'s all')
# remove leading whitespace from barcode
barcode = barcode[1:]
return barcode, barcodeinfo, barcode_found
# get the active image document
activeimage = Zen.Application.Documents.ActiveDocument
# read the barcode from the image
barcode, barcodeinfo, found = ReadBarCodefromImage(activeimage)
print 'Found Barcode : ', found
print 'Barcode : ', barcode
print 'Barcode Info : ', barcodeinfo
if found:
# save with new name
filename = activeimage.FileName
newname = Path.Combine(
Path.GetDirectoryName(filename),
Path.GetFileNameWithoutExtension(filename) + '_' + barcode + '.czi')
print 'Save with new name : ', newname
activeimage.Save(newname)
activeimage.Close()
if reload:
reload_image = Zen.Application.LoadImage(newname, False)
Zen.Application.Documents.Add(reload_image)
print 'Done.'
# check directory for files to export
czidir = Directory.GetFiles(sourcedir, '*.czi')
numczi = czidir.Length
# this list contains the subdirectories created for splitting
splitdirs = []
if split == True:
print 'Split CZI using Split Scenes (Write Files): yes'
# Batch Loop - Load all CZI images and do Split Scenes (Write Files)
for i in range(0, numczi):
# get current CZI file
czifile = czidir[i]
file_woExt = Path.GetFileNameWithoutExtension(czifile)
# create separate directory for the current file
splitdir = Path.Combine(sourcedir, file_woExt + '_Single')
Directory.CreateDirectory(splitdir)
# store directory name inside list
splitdirs.append(splitdir)
print 'File to split: ', czifile
image = Zen.Application.LoadImage(czifile, False)
# split single CZI file containing all wells into single CZI files
Zen.Processing.Utilities.SplitScenes(image, splitdir,
ZenCompressionMethod.None, True,
True, False)
# close file
image.Close()
print 'Finished Split Scences (Write Files): ', czifile
raise Exception('Execution stopped. Required Columns are missing.')
# show and save data tables to the specified folder
Zen.Application.Documents.Add(AllObj)
Zen.Application.Documents.Add(SingleObj)
AllObj.Save(Path.Combine(OutputFolder, 'OverviewTable.csv'))
SingleObj.Save(Path.Combine(OutputFolder, 'SingleObjectsTable.csv'))
# use APEER module to detect the objects
if use_apeer:
# read it from settings file
ams = ZenApeer.Onsite.ModuleSetting()
# loaf the APEER module seeting b - remove *.czams file extension first
ams.Load(Path.GetFileNameWithoutExtension(ApeerMS))
print('----- Apeer Module Setting -----')
print('Module Name : ', ams.ModuleName)
print('Module Version : ', ams.ModuleVersion)
print('Module Parameters : ', ams.Parameters)
# get module and check
mymodule, version_found = get_module(ams.ModuleName,
module_version=ams.ModuleVersion)
# exit if the check failed
if mymodule is None or not version_found:
print('Module check failed. Exiting.')
raise SystemExit
