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Python ResultsTable.getCounter方法代码示例

本文整理汇总了Python中ij.measure.ResultsTable.getCounter方法的典型用法代码示例。如果您正苦于以下问题:Python ResultsTable.getCounter方法的具体用法?Python ResultsTable.getCounter怎么用?Python ResultsTable.getCounter使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在ij.measure.ResultsTable的用法示例。


在下文中一共展示了ResultsTable.getCounter方法的4个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: MandersPlugin

# 需要导入模块: from ij.measure import ResultsTable [as 别名]
# 或者: from ij.measure.ResultsTable import getCounter [as 别名]

#.........这里部分代码省略.........
			image = self.imp
			mode3D = self.checkbox3D.isSelected()
			if image is not None and cell is not None and mode3D:
				roi = cell.slices[selectedSlice].roi
				if (image.z - 1 != selectedSlice):
					image.z = selectedSlice + 1				
				image.setRoi(roi, True)
			if self.preview is not None and not mode3D:
				self.preview.setRoi(cell.roi, True)

	def updateSlice(self, event):
		if self.checkbox3D.isSelected():
			self.updateSlice3D(self.imp)
		else:
			self.updateSlice2D(self.preview)

	def updateSlice3D(self, imp):
		selectedCell = self.cellList.selectedIndex
		selectedSlice = self.sliceList.selectedIndex
		if selectedCell >= 0 and selectedSlice >= 0 and imp is not None:
			cell = self.cells[selectedCell]
			impRoi = imp.getRoi()
			if cell is not None and impRoi is not None:
				index = selectedSlice + 1
				roi = ShapeRoi(impRoi, position = index)
				cell.mode3D = True
				cell.name = "Cell %i (3D)" % cell.n
				cell.slices[selectedSlice].roi = roi
				if (index + 1 <= len(cell.slices)):
					imp.z = index + 1			
			self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell))
			self.sliceList.repaint(self.sliceList.getCellBounds(selectedSlice, selectedSlice))

	def updateSlice2D(self, imp):
		selectedCell = self.cellList.selectedIndex
		if selectedCell >= 0 and imp is not None:
			cell = self.cells[selectedCell]
			impRoi = imp.getRoi()
			if cell is not None and impRoi is not None:
				roi = ShapeRoi(impRoi, position = 1)
				cell.mode3D = False
				cell.name = "Cell %i (2D)" % cell.n
				cell.roi = roi	
			self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell))
	
	def imageOpened(self, imp):
		pass

	def imageClosed(self, imp):
		pass

	def imageUpdated(self, imp):
		if self.checkbox3D.isSelected():
			if imp is not None:
				selectedCell = self.cellList.selectedIndex
				selectedSlice = imp.z - 1
			if imp == self.imp and selectedSlice != self.sliceList.selectedIndex:
				self.sliceList.selectedIndex = selectedSlice

	def doneSelecting(self, event):
		oluts = self.imp.luts
		luts = []
		channels = []
		for c, method in enumerate(self.methods):
			if method != "None":
				luts.append(oluts[c])
				channels.append(c)
		for cell in self.cells:
			manders = self.getManders(self.imp, cell)
			if manders is not None:
				chimps, thrimps, thrs, raws, thrds = manders
				index = self.cells.index(cell) + 1
				title = "Cell_%i-" % index + self.imp.title
				self.saveMultichannelImage(title, chimps, oluts)
				title = "Cell_%i_thrd-" % index + self.imp.title
				self.saveMultichannelImage(title, thrimps, luts)
				self.results.incrementCounter()
				row = self.results.getCounter() - 1
				for i, thr in enumerate(thrs):
					if thr is not None:
						self.results.setValue("Threshold %i" % (i + 1), row, int(thr))
				for i, pair in enumerate(self.pairs):
					self.results.setValue("%i-%i M1 raw" % pair, row, float(raws[i].m1))
					self.results.setValue("%i-%i M2 raw" % pair, row, float(raws[i].m2))
					self.results.setValue("%i-%i M1 thrd" % pair, row, float(thrds[i].m1))
					self.results.setValue("%i-%i M2 thrd" % pair, row, float(thrds[i].m2))
		self.closeImage()
		if not self.processNextFile():
			print "All done - happy analysis!"
			self.results.show("Manders collocalization results")
			self.exit()

	def windowClosing(self, e):
		print "Closing plugin - BYE!!!"
		self.exit()

	def exit(self):
		ImagePlus.removeImageListener(self)
		self.closeImage()
		self.closeMainWindow()
开发者ID:rejsmont,项目名称:FijiScripts,代码行数:104,代码来源:mColoc3D.py

示例2: calculateThreshold

# 需要导入模块: from ij.measure import ResultsTable [as 别名]
# 或者: from ij.measure.ResultsTable import getCounter [as 别名]
		thr1, thrimp1 = calculateThreshold(imp1, roi, methods[0])
		thr2, thrimp2 = calculateThreshold(imp2, roi, methods[1])
		
		cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
		rtype = img1.randomAccess().get().createVariable()
		raw = manders.calculateMandersCorrelation(cursor, rtype)
		rthr1 = rtype.copy()
		rthr2 = rtype.copy()
		rthr1.set(thr1)
		rthr2.set(thr2)
		cursor.reset()
		thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above)
		print "Results are: %f %f %f %f" % (raw.m1, raw.m2, thrd.m1, thrd.m2)

		results.incrementCounter()
		rowno = results.getCounter() - 1
		results.setValue("Cell", rowno, int(rowno))
		results.setValue("Threshold 1", rowno, int(thr1))
		results.setValue("Threshold 2", rowno, int(thr2))
		results.setValue("M1 raw", rowno, float(raw.m1))
		results.setValue("M2 raw", rowno, float(raw.m2))
		results.setValue("M1 thrd", rowno, float(thrd.m1))
		results.setValue("M2 thrd", rowno, float(thrd.m2))
		
		thrimp = RGBStackMerge.mergeChannels([thrimp1, thrimp2], False)
		saver = FileSaver(thrimp)
		saver.saveAsTiffStack(outputDir + "Cell_%i-" % results.getCounter() + title + ".tif")
		thrimp.close()

results.show("Colocalization results")
开发者ID:rejsmont,项目名称:FijiScripts,代码行数:32,代码来源:mcoloc.py

示例3: ResultsTable

# 需要导入模块: from ij.measure import ResultsTable [as 别名]
# 或者: from ij.measure.ResultsTable import getCounter [as 别名]
#    + PA.SHOW_RESULTS \    
rt = ResultsTable()
p = PA(options, PA.AREA + PA.STACK_POSITION, rt, MINSIZE, MAXSIZE)
p.setHideOutputImage(True)

# Morphological dilate
binner.setup('dilate', None)


clusters = 0
initialCells = 0

# dilate by 'SAMPLEITER'
for i in range(SAMPLEITER+1):
	p.analyze(binimp)
	cellcounts = rt.getCounter()
	if i == 0:
		initialCells = cellcounts
	#IJ.log("iter:" + str(i) + " -- cell counts: " + str(cellcounts))
	if i == SAMPLEITER:
		clusters = cellcounts
	binner.run(binimp.getProcessor())
	rt.reset()

#binimp.show()
#binorg.show()
IJ.log("==== " + imp3.getTitle() + " =====")
IJ.log("Number of Nucleus : " + str(initialCells))
IJ.log("Clusters at dilation " + str(SAMPLEITER) + ": " + str(clusters))
IJ.log("Clusters/Nucleus " + str(float(clusters)/float(initialCells)))
开发者ID:cmci,项目名称:CellClusterIndex,代码行数:32,代码来源:ClusterIndex.py

示例4: main

# 需要导入模块: from ij.measure import ResultsTable [as 别名]
# 或者: from ij.measure.ResultsTable import getCounter [as 别名]

#.........这里部分代码省略.........
    t_rows = rt.getColumnAsDoubles(t_col)

    # Assess n of data points and extract unique path ids
    n_rows = len(track_id_rows)
    row_indices = range(n_rows)
    track_ids = set(track_id_rows)
    n_tracks = len(track_ids)
    log("Table has %g rows" % n_rows)
    log("Table has %g tracks" % n_tracks)

    log("Parsing tracks...")
    for track_id in track_ids:


        for row, next_row in zip(row_indices, row_indices[1:]):

            if track_id_rows[row] != track_id:
                continue

            if not isNumber(angle_rows[row]):
                 rt.setValue("FLAG", row, "NA")
                 continue

            lower_bound = max(0, row - BOUT_WINDOW + 1)
            upper_bound = min(n_rows-1, row + BOUT_WINDOW)
            win_d2p = []
            for _ in range(lower_bound, upper_bound):
                win_d2p.append(d2p_rows[row])

            if sum(win_d2p) <= MIN_D2P * len(win_d2p):
                rt.setValue("FLAG", row, 0)

            else:
                current_angle = angle_rows[row]
                next_angle = angle_rows[next_row]
                current_delta = delta_rows[row]

                flag = -1 if current_angle < 0 else 1
                delta_change = (abs(current_delta) > 90)
                same_sign = ((current_angle<0) == (next_angle<0))
                if delta_change and not same_sign:
                    flag *= -1

                rt.setValue("FLAG", row, flag)
                if next_row == n_rows - 1:
                    rt.setValue("FLAG", next_row, flag)

    if rt.save(table_file.getAbsolutePath()):
        log("Processed table successfully saved (file overwritten)")
    else:
        log("Could not override input file. Displaying it...")
        rt.show(table_file.name)


    log("Creating onset table...")
    onset_rt = RT()
    onset_rt.showRowNumbers(False)

    frame_int = DEF_FRAME_INTERVAL
    if "table" in frame_rate_detection:
        frame_int = getFrameIntervalFromTable(row_indices, track_id_rows, t_rows)
    elif "image" in frame_rate_detection:
        frame_int = getFrameIntervalFromImage(image_file.getAbsolutePath())
    else:
        log("Using default frame rate")

    for track_id in track_ids:

        for prev_row, row in zip(row_indices, row_indices[1:]):

            if not track_id in (track_id_rows[prev_row], track_id_rows[row]):
                continue

            flag = rt.getValue("FLAG", row)
            if not isNumber(flag):
                continue

            flag = int(flag)
            if flag == 0:
                continue

            if flag == 1 or flag == -1:
                srow = onset_rt.getCounter()
                onset_rt.incrementCounter()
                onset_rt.setValue("TID", srow, track_id)
                from_frame = int(t_rows[prev_row]/frame_int) + 1
                to_frame = int(t_rows[row]/frame_int) + 1
                onset_rt.setValue("First disp. [t]", srow,
                    "%s to %s" % (t_rows[prev_row], t_rows[row]))
                onset_rt.setValue("First disp. [frames]", srow,
                    "%s to %s" % (from_frame, to_frame))
                onset_rt.setValue("ManualTag", srow, "")
                break

    out_path = suffixed_path(table_file.getAbsolutePath(), "ManualTagging")
    if onset_rt.save(out_path):
        log("Summary table successfully saved: %s" % out_path)
    else:
        log("File not saved... Displaying onset table")
        onset_rt.show("Onsets %s" % table_file.name)
开发者ID:tferr,项目名称:Scripts,代码行数:104,代码来源:Tag_and_Onset_MtrackJ_paths.py


注:本文中的ij.measure.ResultsTable.getCounter方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。