def render_subtitle(element, elements):
if hasattr(
element, "subtitle"
) and element.config["subtitle_type"] == "render" and element.subtitle:
subtitle = gst.element_factory_make("textoverlay")
elements.append(subtitle)
Annotate.add_subtitle(element, subtitle, element.subtitle,
element.config)
def getCellTypes(self):
"""
Annotates single cell types at each level and adds the result to the object.
"""
scData = Utils.convertAnnDataToDf(self.scData)
scData = scData.loc[self._genesIntersect]
refDataset = self.refDataset.loc[self._genesIntersect]
self.scAnnot = Annotate.annotateCells(scData, refDataset,
self.refAnnot, self.deAll)
self.scData.obs["cellType"] = self.scAnnot["cellType"]
def get_bin(self, duration=None):
if duration is None:
duration = self.duration
src = gst.element_factory_make("videotestsrc")
src.props.pattern = "black"
src.props.foreground_color = 0;
src.props.background_color = 0;
caps= gst.element_factory_make("capsfilter")
caps.props.caps = self.config.get_video_caps("AYUV")
elements = [src, caps]
if self.name == "titlebar":
if self.title1:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title1, "top_title", self.config)
elements.append(textoverlay)
if self.title2:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title2, "bottom_title", self.config)
elements.append(textoverlay)
else:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title1, "title", self.config)
elements.append(textoverlay)
process_effects(self, duration, elements)
bin = gst.Bin()
bin.add(*elements)
gst.element_link_many(*elements)
bin.add_pad(gst.GhostPad("src", elements[-1].get_pad("src")))
return bin
def process_effects(element, duration, elements, custom_config={}):
#if not(custom_config):
# caps = gst.element_factory_make("capsfilter")
# elements.append(caps)
# caps.set_property("caps", element.config.get_video_caps("AYUV", custom_config))
# elements.append(gst.element_factory_make("ffmpegcolorspace"))
# #elements.append(gst.element_factory_make("frei0r-filter-bw0r"))
# #elements.append(gst.element_factory_make("frei0r-filter-cartoon"))
# #elements.append(gst.element_factory_make("frei0r-filter-scale0tilt"))
# elements.append(gst.element_factory_make("agingtv"))
# elements.append(gst.element_factory_make("ffmpegcolorspace"))
# caps = gst.element_factory_make("capsfilter")
# elements.append(caps)
# caps.set_property("caps", element.config.get_video_caps("AYUV",custom_config))
Annotate.add_annotations(element, duration, elements)
render_subtitle(element, elements)
caps = gst.element_factory_make("capsfilter")
elements.append(caps)
caps.set_property("caps", element.config.get_video_caps("AYUV", custom_config))
for gst_element in elements:
if gst_element.get_name().startswith("kenburns"):
KenBurns.configure_kenburns(element, gst_element, duration)
def process_effects(element, duration, elements, custom_config={}):
#if not(custom_config):
# caps = gst.element_factory_make("capsfilter")
# elements.append(caps)
# caps.set_property("caps", element.config.get_video_caps("AYUV", custom_config))
# elements.append(gst.element_factory_make("ffmpegcolorspace"))
# #elements.append(gst.element_factory_make("frei0r-filter-bw0r"))
# #elements.append(gst.element_factory_make("frei0r-filter-cartoon"))
# #elements.append(gst.element_factory_make("frei0r-filter-scale0tilt"))
# elements.append(gst.element_factory_make("agingtv"))
# elements.append(gst.element_factory_make("ffmpegcolorspace"))
# caps = gst.element_factory_make("capsfilter")
# elements.append(caps)
# caps.set_property("caps", element.config.get_video_caps("AYUV",custom_config))
Annotate.add_annotations(element, duration, elements)
render_subtitle(element, elements)
caps = gst.element_factory_make("capsfilter")
elements.append(caps)
caps.set_property("caps",
element.config.get_video_caps("AYUV", custom_config))
for gst_element in elements:
if gst_element.get_name().startswith("kenburns"):
KenBurns.configure_kenburns(element, gst_element, duration)
def get_bin(self, duration=None):
if duration is None:
duration = self.duration
src = gst.element_factory_make("videotestsrc")
src.props.pattern = "black"
src.props.foreground_color = 0
src.props.background_color = 0
caps = gst.element_factory_make("capsfilter")
caps.props.caps = self.config.get_video_caps("AYUV")
elements = [src, caps]
if self.name == "titlebar":
if self.title1:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title1, "top_title",
self.config)
elements.append(textoverlay)
if self.title2:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title2,
"bottom_title", self.config)
elements.append(textoverlay)
else:
textoverlay = gst.element_factory_make("textoverlay")
Annotate.add_title(self, textoverlay, self.title1, "title",
self.config)
elements.append(textoverlay)
process_effects(self, duration, elements)
bin = gst.Bin()
bin.add(*elements)
gst.element_link_many(*elements)
bin.add_pad(gst.GhostPad("src", elements[-1].get_pad("src")))
return bin
axes = axs.AxesSequence()
for i,ax in zip(range(axialPETIM.shape[0]),axes):
ax.imshow(axialPETIM[i,:,:],cmap='hot',interpolation='bicubic')
ax.set_title('zlice: {}'.format(i))
axes.show()
zslices = axes.selected_slices
del axes
Nslice = zslices[1]-zslices[0]+1
center_zslice = int(zslices[0] + 0.5*Nslice)
theIM = axialPETIM[center_zslice,:,:]
plt.imshow(theIM,cmap='hot',interpolation='bicubic')
a = ant.Annotate()
plt.show()
# plot the ROI image
rx0,ry0,rx1,ry1=[int(val) for val in [a.x0,a.y0,a.x1,a.y1]]
theROI = theIM[ry0:ry1,rx0:rx1]
plt.imshow(theROI,cmap='hot',interpolation='bicubic')
plt.show()
print rx0,ry0,rx1,ry1
# double check if the VOI covers the entire tumor
for n in range(zslices[0],zslices[1],1):
theROI = axialPETIM[n,ry0:ry1, rx0:rx1]
plt.imshow(theROI,cmap='hot',interpolation='bicubic')
plt.show()
def main():
fdir = sys.argv[1]
imdir = int(sys.argv[2])
Nslice = int(sys.argv[3])
soffset = int(sys.argv[4])
isscrecon = int(sys.argv[5])
# Get a DICOM volume
if isscrecon == 0:
xc, yc, zc, dxyz, nxyz, vol = GetDcmVol(fdir, False)
else:
xc, yc, zc, dxyz, nxyz, vol = GetDcmVol(fdir)
print xc, yc, zc, nxyz
# Get an image in a given direction and show the image
if imdir == 2:
imindx = xc - 10
elif imdir == 0:
imindx = zc
else:
imindx = yc
theIM = ivfit.Get2DPlane(vol, imdir, imindx + soffset)
plt.imshow(theIM, cmap='hot', interpolation='bicubic')
print theIM.shape
# Select a ROI in the image
a = ant.Annotate()
plt.show()
# plot the ROI image
rx0, ry0, rx1, ry1 = [int(val) for val in [a.x0, a.y0, a.x1, a.y1]]
theROI = theIM[ry0:ry1, rx0:rx1]
plt.imshow(theROI, cmap='hot', interpolation='bicubic')
# get the correct pixel dimension
thedxyz = np.take(dxyz, [2, 1, 0])
theiax = np.arange(len(thedxyz))
oh = theiax[theiax != imdir]
thedxy = np.take(thedxyz, oh)
print thedxy
statscombo1 = np.empty((Nslice + 2, 5))
statscombo2 = np.empty((Nslice + 2, 5))
# determine the slice # to look at
halfNslice = int(math.floor(Nslice / 2.))
imindx0 = imindx + soffset
if Nslice % 2. == 0:
lnslice = np.arange(imindx0 - halfNslice, imindx0 + halfNslice, 1)
else:
lnslice = np.arange(imindx0 - halfNslice, imindx0 + halfNslice + 1, 1)
for ii in range(len(lnslice)):
if ii == 0:
ioi = theROI
else:
theIM = ivfit.Get2DPlane(vol, imdir, lnslice[ii])
ioi = theIM[ry0:ry1, rx0:rx1]
for ldir in range(2):
# Get the line spread function of the ROI image
xdata, ydata, demoim = ivfit.ShowLineProfile(ioi, ldir)
plt.imshow(demoim, cmap='hot', interpolation='bicubic')
xfit, yfit, A, x0, sigma, r2, fwhm = ivfit.GaussFit_lsq(
xdata, ydata, thedxy[ldir], isplot=True)
print A, x0, sigma, 'Gaussian fit r2 = {}, FWHM = {} mm'.format(
r2, fwhm)
if ldir == 0:
statscombo2[ii, :] = [A, x0, sigma, r2, fwhm]
else:
statscombo1[ii, :] = [A, x0, sigma, r2, fwhm]
# append the mean and stdev
statscombo1[-2] = np.mean(statscombo1[:-2], axis=0, dtype=np.float64)
statscombo1[-1] = np.std(statscombo1[:-2], axis=0, dtype=np.float64)
statscombo2[-2] = np.mean(statscombo2[:-2], axis=0, dtype=np.float64)
statscombo2[-1] = np.std(statscombo2[:-2], axis=0, dtype=np.float64)
statsall = np.hstack((statscombo1, statscombo2))
# get all the info into a data frame
rowname = [str(i) for i in lnslice] + ['mean', 'stdev']
#print rowname
if imdir == 0:
colname = [
'A', 'x0', 'sigma', 'R2', 'X-dir FWHM (mm)', 'A', 'x0', 'sigma',
'R2', 'Y-dir FWHM (mm)'
]
elif imdir == 2:
colname = [
'A', 'x0', 'sigma', 'R2', 'Y-dir FWHM (mm)', 'A', 'x0', 'sigma',
'R2', 'Z-dir FWHM (mm)'
]
df = ps.DataFrame(statsall, index=rowname, columns=colname)
wfdir = '/Users/shuang/Documents/Proj_PETMR/Data/Measurement_SpatRes'
froot = '/Users/shuang/Documents/Proj_PETMR/IM'
tmp = re.findall(r'{}/(.+)*'.format(froot), fdir)
if tmp: # make sure the fdir string can be parsed
tag = tmp[0].replace('/', '_')
file = '{}/SpaRes_{}.csv'.format(wfdir, tag)
df.to_csv(file)
def render_subtitle(element, elements):
if hasattr(element, "subtitle") and element.config["subtitle_type"] == "render" and element.subtitle:
subtitle = gst.element_factory_make("textoverlay")
elements.append(subtitle)
Annotate.add_subtitle(element, subtitle, element.subtitle, element.config)
def main():
fdir = sys.argv[1]
imdir = int(sys.argv[2])
soffset = int(sys.argv[3])
isscrecon = int(sys.argv[4])
# Get a DICOM volume
if isscrecon == 0:
xc, yc, zc, dxyz, nxyz, vol = GetDcmVol(fdir, False)
else:
xc, yc, zc, dxyz, nxyz, vol = GetDcmVol(fdir)
print xc, yc, zc, nxyz
# Get an image in a given direction and show the image
if imdir == 2:
imindx = xc - 10
elif imdir == 0:
imindx = zc
else:
imindx = yc
theIM = ivfit.Get2DPlane(vol, imdir, imindx + soffset)
plt.imshow(theIM, cmap='hot', interpolation='bicubic')
print theIM.shape
# Select a ROI in the image
a = ant.Annotate()
plt.show()
# plot the ROI image
rx0, ry0, rx1, ry1 = [int(val) for val in [a.x0, a.y0, a.x1, a.y1]]
theROI = theIM[ry0:ry1, rx0:rx1]
plt.imshow(theROI, cmap='hot', interpolation='bicubic')
# get the correct pixel dimension
thedxyz = np.take(dxyz, [2, 1, 0])
theiax = np.arange(len(thedxyz))
oh = theiax[theiax != imdir]
thedxy = np.take(thedxyz, oh)
# get the line profile and fit a Gaussian via leastsq
#wfdir = '/Users/shuang/Documents/Proj_PETMR/Data/Measurement_SpatRes'
wfdir = '/Users/shuang/Documents/UCSF/Conference/IEEE2014/Poster'
# get file tag
froot = '/Users/shuang/Documents/Proj_PETMR/IM'
tmp = re.findall(r'{}/(.+)*'.format(froot), fdir)
if tmp: # make sure the fdir string can be parsed
tag = tmp[0].replace('/', '_')
# save the original ROI image
fig = plt.figure(1, figsize=(10, 10))
ax = fig.add_subplot(111)
plt.imshow(theROI, cmap='hot', interpolation='bicubic')
plt.xticks([])
plt.yticks([])
imname = '{}/theROI_{}.pdf'.format(wfdir, tag)
print imname
plt.savefig(imname)
for ldir in range(2):
# Get the line spread function of the ROI image
xdata, ydata, demoim = ivfit.ShowLineProfile(theROI, ldir)
nydata = ydata / np.amax(ydata)
fig = plt.figure(2, figsize=(8, 8))
ax = fig.add_subplot(111)
plt.imshow(demoim, cmap='hot', interpolation='bicubic')
imname = '{}/demoim_{}_imdir{:d}_ldir{:d}.pdf'.format(
wfdir, tag, imdir, ldir)
print imname
plt.savefig(imname)
xfit, yfit, A, x0, sigma, r2, fwhm = ivfit.GaussFit_lsq(
xdata, nydata, thedxy[ldir])
print A, x0, sigma, 'Gaussian fit r2 = {}, FWHM = {} mm'.format(
r2, fwhm)
print xfit, yfit
#wfname1 = '{}/LSP_{}_imdir{:d}_ldir{:d}.txt'.format(wfdir,tag,imdir,ldir)
#np.savetxt(wfname1,(xdata[:,np.newaxis],ydata[:,np.newaxis]),delimiter='\t')
#wfname2 = '{}/fitLSP_{}_imdir{:d}_ldir{:d}.txt'.format(wfdir,tag,imdir,ldir)
#np.savetxt(wfname2,(xfit,yfit),delimiter='\t')
# plot the profile
fig = plt.figure(3, figsize=(11, 8))
ax = fig.add_subplot(111)
plt.rc('lines', linewidth=3)
plt.rc('axes', linewidth=3)
plt.tick_params(labelsize=20)
pixdim = 10 * dxyz[0]
p1 = plt.plot(pixdim * xdata,
nydata,
linestyle='None',
color='b',
marker='o',
markersize=6.0,
label='Original Data')
p2 = plt.plot(pixdim * xfit,
yfit,
color='r',
marker='None',
label='Fitted Data')
axes = plt.gca()
axes.set_ylim([0, np.amax(yfit)])
plt.xlabel('Distance (mm)', fontsize=30)
plt.ylabel('Relative intensity', fontsize=30)
plt.legend(fontsize=30, loc='best')
figname = '{}/LSP_{}_imdir{:d}_ldir{:d}.pdf'.format(
wfdir, tag, imdir, ldir)
print figname
plt.savefig(figname)
plt.show()
def contextMenuEvent(self, event):
menu = QMenu(self) #creates a menu that opens when table is right-clicked
###Options added to menu###
boxAction = menu.addAction("Box Plot")
scatterAction = menu.addAction("Scatter Plot")
menu.addSeparator()
AnnotateAction = menu.addAction("Annotate")
menu.addSeparator()
ReNameAction = menu.addAction("Rename")
printNameAction = menu.addAction("Name?")
printAction = menu.addAction("Print Row")
menu.addSeparator()
resetAction = menu.addAction("Reset Table")
quitAction = menu.addAction("Close Table")
menu.addSeparator()
checkAttributesAction = menu.addAction("Properties") ###checkAttributes open a settings-esque window
action = menu.exec_(self.mapToGlobal(event.pos())) #tracks the mouse and saves the position of an event(action)
if action == quitAction: #close table
self.deleteLater()
elif action == printAction: #outputs the selected row to the console
self.selected = self.selectedItems() #selected items refers to the selection behavior and will be a row of QTable items
n = len(self.selected)
print("n is {}".format(n))
# to use Qtable Items must be converted from item -> string -> float
for i in range(n):
self.selected[i] = str(self.selected[i].text())
for i in range(n):
self.selected[i] = float(self.selected[i])
print(self.selected)
###Attribute Naming related actions###
elif action == resetAction: #if any changes (i.e removing value from Qtable) user can reset to its original data
for i in range(self.LenRowIndex):
# DataValues grabs a row of data from dataframe
DataValues = self.data.iloc[i, :]
print("values are {}".format(DataValues))
# converts these values into list format
ValList = DataValues.values.tolist()
# loops through DataValues list and assigns it to the appropriate cell in the QTable, to 3 significant digits
for j in range(0, self.LenColHeaders):
item = QTableWidgetItem(str(round(ValList[j], 6)))
self.setItem(i, j, item)
elif action == ReNameAction: #action lets you change the name of the table
self.openPop = TableUI.TablePopup() #create an instance of the tableUI
self.openPop.show()
self.openPop.TableString.connect(self.RenameTable) #runs the rename method
elif action == checkAttributesAction:
print("Opening table properties")
self.selected = self.selectedItems() #sets variable selected to be the row highlighted when clicked
self.Row_Selection = self.row(self.selected[1])
print(self.Row_Selection)
try:
#create object using module TableAttritbutesWin.py, pass arg table name, statistics, row index number
self.AttributesWindow = TableAttributesWin.AttributesDialog(self.name, self.StatsInfo,self.Row_Selection)
self.AttributesWindow.show()
except Exception as TableAttErr:
print("error occured when creating the Table Attritbute window.......ERROR: {}".format(TableAttErr))
elif action == printNameAction:
#returns name of table via console
print(self.name)
elif action == AnnotateAction:
print("Annotation has been called")
self.AnnotatedWin = Annotate.TextBoxAnnotation()
self.AnnotatedWin.exec_()
self.AnnotationList.append(self.AnnotatedWin.Annotation)
print(self.AnnotationList)
print("annotations have been appended to list")
self.AnnotationSignal.emit(self.AnnotationList)
print("signal has been emitted")
###GRAPHING COMMANDS###
elif action == boxAction:
print("Box Plot Called from context menu")
try:
self.selected = self.selectedItems()
self.RowNum = self.currentRow() #reports what row of the QtableWidget we selected
print(self.RowNum)
n = len(self.selected)
for i in range(n):
self.selected[i] = str(self.selected[i].text())
for i in range(n):
if self.selected[i] != "": #if the selected has empty string values they are replace with float nulls
self.selected[i] = float(self.selected[i])
else:
self.selected[i] = np.nan
pass
print("right before plotter called")
self.BoxDataSignal.emit(self.selected, self.StatsInfo, self.RowNum) #emit signal carrying all the data to be plotted
except Exception as boxSignalErr:
print("Right when box plot is called an error cccurs and crashes the program. ERROR: {}".format(boxSignalErr))
elif action == scatterAction:
print("Scatter Plot Called from context menu")
self.selected = self.selectedItems()
n = len(self.selected)
for i in range(n):
self.selected[i] = str(self.selected[i].text())
for i in range(n):
if self.selected[i] != "":
self.selected[i] = float(self.selected[i])
else:
self.selected[i] = np.nan
pass
print("right before plotter called")
self.ScatterDataSignal.emit(self.selected, self.ColHeaders) #emit signal carrying all the data to be plotted
else:
print("A menu action was not clicked")
