def export(runs,sortby,flipper,minmon=16):
data = load(runs)
keys = data.keys()
if sortby is None:
values = [""]
else:
values = set([x[sortby] for x in keys])
base = basedir + "%04i/" % runs[-1]
for value in values:
ups = [x for x in keys if x[flipper][0] != '-'
and (sortby is None or x[sortby] == value)]
downs = [x for x in keys if x[flipper][0] == '-'
and (sortby is None or x[sortby] == value)]
if ups != []:
Combiner.save(base+value+"up.pel",
minmon,
ups,
data)
if downs != []:
Combiner.save(base+value+"down.pel",
minmon,
downs,
data)
def onSave(self,event):
#Combine each flipper current
dlg = wx.FileDialog(self,"Save PEL file",wildcard="PEL file|*.pel",
style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal()!=wx.ID_OK:
return
outfile = dlg.GetPath()
minmon = float(self.monctrl.GetValue())#Monitor cutoff for live beam
index = self.currentbox.GetSelections()
keys = [eval(self.currentbox.GetItems()[i]) for i in index]
Combiner.save(outfile,minmon,keys,self.runsets)
def Combiner(self):
print "Assigning scores to evidence..."
assignscore.AssignScore(self.periodicity_output2gff3,self.weightPeriod)
assignscore.AssignScore(self.naivepred_output2gff3,self.weightNaive)
assignscore.AssignScore(self.gtf2gff3_rnaoutput,self.weightRNA)
print "Combining evidence..."
results = Combiner.combine(self.periodicity_output2gff3,self.naivepred_output2gff3,self.gtf2gff3_rnaoutput,self.glimmer_predict2gff3)
self.outputgff3 = self.genomeinput[:-len(".fasta")]+".gff3"
print "Writing results..."
assignscore.writeResults2gff3(results,self.outputgff3,self.seqname_fasta,self.seqname_Combiner)
def onLoad(self,event):
"""Combine the manifests"""
paths = self.listbox.GetItems()
runsets = Combiner.load(paths)
currents = set(runsets.keys())
for current in currents:
self.currentbox.Insert(str(current),0)
self.runsets = runsets
def export(runs,minmon=16):
data = load(runs)
keys = data.keys()
base = basedir + "%04i/" % runs[-1]
#phase(2) controls the cryo-flipper and sample(3) controls the
#v-coil flipper
#
#w -> all flippers on
#x -> cryo flipper on
#y -> solenoid flipper on
#z -> all flippers off
w = [k for k in keys if float(k[2])<0
and float(k[3])<0]
y = [k for k in keys if float(k[2])<0
and float(k[3])>0]
x = [k for k in keys if float(k[2])>0
and float(k[3])<0]
z = [k for k in keys if float(k[2])>0
and float(k[3])>0]
print w
print x
print y
print z
if w != []:
Combiner.save(base+"w_new.pel",
minmon,
w,
data)
if x != []:
Combiner.save(base+"x_new.pel",
minmon,
x,
data)
if y != []:
Combiner.save(base+"y_new.pel",
minmon,
y,
data)
if z != []:
Combiner.save(base+"z_new.pel",
minmon,
z,
data)
def two_flipper(runs, flipper1, flipper2, minmon, current, \
watch="2"):
data = load(runs,current)
keys = data.keys()
values = [""]
base = basedir + "SESAME_%i/" % runs[-1]
for value in values:
if type(value) is not str:
value = normalize_name(value)
upup = [x for x in keys if x[flipper1] < 0 and x[flipper2] < 0 \
and x[choices[watch]]==current]
updown = [x for x in keys if x[flipper1] < 0 and x[flipper2] > 0 \
and x[choices[watch]]==current]
downup = [x for x in keys if x[flipper1] > 0 and x[flipper2] < 0 \
and x[choices[watch]]==current]
downdown = [x for x in keys if x[flipper1] > 0 and x[flipper2] > 0 \
and x[choices[watch]]==current]
if filter is not None:
value = "" #Don't put values on files when we're only running a single export
if upup != []:
print "-------------- Up/Up state --------------"
Combiner.save(base+value+"upup_current=" + str(current),
minmon,
upup,
data)
if updown != []:
print "-------------- Up/Down state --------------"
Combiner.save(base+value+"updown_current=" + str(current),
minmon,
updown,
data)
if downup != []:
print "-------------- Down/Up state --------------"
Combiner.save(base+value+"downup_current=" + str(current),
minmon,
downup,
data)
if downdown != []:
print "-------------- Down/Down state --------------"
Combiner.save(base+value+"downdown_current=" + str(current),
minmon,
downdown,
data)
if [upup,updown,downup,downdown]==[[],[],[],[]]:
print("No data to write")
def export(runs,sortby=None,flipper=0,minmon=8,current=None,\
filter=None,watch=None):
data = load(runs,current)
keys = data.keys()
print keys
#
if sortby is None:
values = [""]
else:
if filter is None:
values = set([x[sortby] for x in keys])
else:
values = [filter]
#
base = basedir + "SESAME_%i/" % runs[-1]
#
for value in values:
if type(value) is not str:
value = normalize_name(value)
ups = [x for x in keys if (flipper is None or x[flipper] < 0) \
and (watch is None or x[choices[watch]]==current) \
and (sortby is None or normalize_name(x[sortby]) == value)]
downs = [x for x in keys if (flipper is not None and x[flipper] > 0) \
and (watch is None or x[choices[watch]]==current) \
and (sortby is None or normalize_name(x[sortby]) == value)]
sames = [x for x in keys if (flipper is not None and x[flipper] == 0) \
and (watch is None or x[choices[watch]]==current) \
and (sortby is None or normalize_name(x[sortby]) == value)]
#
if filter is not None:
value = "" #Don't put values on files when we're only running a single export
#
if current==None:
titleend=""
else:
titleend="_current="+str(current)
#
if ups == [] and downs == []:
Combiner.save(base+value+"Combined"+titleend,
0,
sames,
data)
if ups != []:
print "-------------- Up state --------------"
Combiner.save(base+value+"up"+titleend,
minmon,
ups,
data)
if downs != []:
print "-------------- Down state --------------"
Combiner.save(base+value+"down"+titleend,
minmon,
downs,
data)
def main():
#calib = calibration.calibration(visualtion=True)
base_dataset_path = os.path.join(os.getcwd(), "datasets", "test_lab6")
file_name = os.path.join(base_dataset_path, "imageData.txt")
image_directory = base_dataset_path
drone_location = os.path.join(base_dataset_path, "drone_postion.txt")
write_img_dir_path = os.path.join(base_dataset_path, "results")
all_images, data_matrix = util.importData(file_name, drone_location,
image_directory)
all_images = all_images[:12]
data_matrix = data_matrix[:12]
# for i in range(0,3):
# all_images[i] = all_images[i][::10, ::10, :]
#all_imgs_undistorted = calib.calibrate(all_images)
# stitcher = cv2.createStitcher() if imutils.is_cv3() else cv2.Stitcher_create()
# (status, stitched) = stitcher.stitch(all_images)
my_combiner = Combiner.Combiner(all_images, data_matrix)
result = my_combiner.createMosaic()
util.display("RESULT", result)
if not os.path.exists(write_img_dir_path):
os.makedirs(write_img_dir_path)
cv2.imwrite(os.path.join(write_img_dir_path, "finalResult3.png"), result)
if os.path.isdir('results') == True:
os.rename('results', 'results - ' + str(now))
os.mkdir('results')
fileName = "datasets/imageData.txt"
imageDirectory = "datasets/images/"
print("Creating Temp Directory")
if os.path.isdir('temp') == True:
shutil.rmtree('temp', ignore_errors=False, onerror=None)
os.mkdir('temp')
print("Copying Images to Temp Directory")
allImages, dataMatrix = util.importData(fileName, imageDirectory)
# Perspective.changePerspective(allImages, dataMatrix)
print("Sitiching Images")
start = time.time()
result = Combiner.combine()
end = time.time()
util.display("RESULT", result, 4000000)
cv2.imwrite("results/final_result.jpg", result)
print("Time --->>>>>", end - start)
print("Done. Find your final image in results folder as final_result.jpg")
def load(runs):
paths = [basedir + "%04i/Manifest.xml"
% run for run in runs]
return Combiner.load(paths)
'''
Driver script. Execute this to perform the mosaic procedure.
'''
import utilities as util
import Combiner
import cv2
fileName = "datasets/imageData.txt"
imageDirectory = "datasets/images/"
allImages, dataMatrix = util.importData(fileName, imageDirectory)
myCombiner = Combiner.Combiner(allImages, dataMatrix)
result = myCombiner.createMosaic()
util.display("RESULT", result)
cv2.imwrite("results/finalResult.png", result)
def load(runs,current=None):
paths = [basedir + "SESAME_%i/SESAME_%i_runinfo.xml"
% (run,run) for run in runs]
return Combiner.load(paths,current)
