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类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()
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")
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)))
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)