def process(pth):
print(f'\nProcessing {pth}')
save_pth = pth / 'intra_reg_stacks'
try:
save_pth.mkdir()
except FileExistsError:
ex('Save File for reg stacks already exists. Delete and re-run.')
#Intravolume registration of the fixed volume
print('Doing intravolume registration.')
files = sorted(list(pth.glob('*.tif')), key=sort_key)
#files = list(pth.glob('*.tif'))
loop_starts = time.time()
for file in files:
start_time = time.time()
print(f'Processing: {file}')
fixed = io.imread(str(file))
fixed = flat.fix(fixed[:, :, :512], divisor=4)
save_name = save_pth / f'intra_reg_{file.name}'
io.imsave(arr=fixed.astype('float32'), fname=str(save_name))
end_time = time.time()
print(f'{file} was processed in {(end_time - start_time):.2f}s. \
\n{((end_time - loop_starts)/60):.2f} minutes have elapsed.')
def main():
source = askdirectory()
if source == '':
ex("\n\nExited: No file path selected\n\n")
#sorting(Path(os.path.abspath(source)))
process(Path(source))
print('\n\n\n\t\t\t\t---------\n\t\t\t\tCompleted\n\t\t\t\t---------')
def process(pth):
print(f'\nProcessing {pth}')
save_pth = pth / 'reg_stacks'
#tmat_pth = pth / 'transformation_matrices'
try:
save_pth.mkdir()
#tmat_pth.mkdir()
except FileExistsError:
ex('Save File for reg stacks or tmats already exists. Delete and re-run.'
)
#tell pystack reg that we will use a translational transformation
#there shouldn't be intra-volume rotation or shear (there might be for rod blink)
sr = StackReg(StackReg.TRANSLATION)
#register to the first slice and output the transfomation matrix without transforming
#iterate through the files in the stacks folder
files = pth.glob('*.tif')
loop_starts = time.time()
for i, file in enumerate(files):
#start_time = time.time()
print(f'Processing: {file}')
#Intravolume registration of the fixed volume
#load first stack and do a 3d gaussian blur with a sigma=1
#str needed for imread, otherwise only one frame is loaded
fixed = io.imread(str(file)) #had gauss(), testing
t_mats = sr.register_stack(gauss(fixed), reference='first', n_frames=1)
#remove the x shift from all the matrices - horizontal movement isn't relevant here,
#the volume should be acquired quickly enough that this isn't a problem.
t_mats[:, 0, -1] = 0
fixed = sr.transform_stack(fixed, tmats=t_mats)
#Using previous to see if I could get rid of wigge. Didn't seem to work.
#t_mats = sr.register_stack(gauss(fixed), reference='previous')
#t_mats[:,1,-1] = 0
#fixed = sr.transform_stack(fixed, tmats=t_mats)
#save the register fixed volume in the parent directory for reference
save_name = save_pth / f'reg_{file.name}'
#io.imsave(arr=img_as_uint(fixed), fname=str(save_name))
io.imsave(arr=img_as_float32(fixed), fname=str(save_name))
#get fixed out of memory - may not be worth the time?
print(f'Intravolume registration complete. File saved at {save_name}')
#end_time = time.time()
#print(f'{file} was processed in {(end_time - start_time):.2f}s. \
#\n{((end_time - loop_starts)/60):.2f} minutes have elapsed.')
#de;ete emumerate
#if i==4:
#ex('auto break')
end_time = time.time()
print(f'Run took {(end_time-loop_starts)/60:.2f} minutes')
def main():
source = askdirectory()
if source == '':
ex("\n\nExited: No file path selected\n\n")
#sorting(Path(os.path.abspath(source)))
src = Path(source)
stack = im_open(src)
avg_stack = timeseries(stack)
save_pth = src / 'timeseries'
save_pth.mkdir()
io.imsave(arr=img_as_float32(avg_stack),
fname=str(save_pth / 'timeseries.tif'))
print('\n\n\n\t\t\t\t---------\n\t\t\t\tCompleted\n\t\t\t\t---------')
def dependency_check():
# pylint: disable=import-outside-toplevel
# fmt: off
try:
import oead
del oead
except ImportError:
from platform import system
if system() == "Windows":
native_msg(
"The latest (2019) Visual C++ redistributable is required to run BCML. "
"Please download it from the following link and try again:\n"
"https://aka.ms/vs/16/release/vc_redist.x64.exe",
"Dependency Error")
from sys import exit as ex
ex(1)
def im_open(pth):
"""Imports a folder containing a stack of images using scikit image collections"""
try:
#Double check to make sure pth is a directory.
assert pth.is_dir()
#Get list of tif files in pth and sort based on 'stem' which is the index of the B-scan (i.e. y position)
#files = sorted(pth.glob('*.tif'), key=sort_key)
#load the collection
raw_stack = io.imread_collection(str(pth / '*.tif'))
#turn them into a stack that can be manipulated as a multdimensional array.
stack = io.collection.concatenate_images(raw_stack)
return stack
except AssertionError:
#if the assert fails the program stops. This is a bit heavy handed...
ex("A non-directory object was given to the __open__ function")
def main ():
if len (argv) < 4:
print 'Use: memeorystar.py <value> <type> <pid>'
ex (-1)
op = OptionParser ('memorystar.py <value> <type> <pid>')
op.add_option ('-G', '--graph', default=False, action='store_true', dest='graph', help='if you want to use GTK interface use this option')
(op, args) = op.parse_args ()
if op.graph:
window = gt.MainWindow ()
window.main ()
else:
dbg = ProcessDebugger (argv [-1])
if argv [-2] == 'boolean': print dbg.search_boolean_value (argv [-3])
elif argv [-2] == 'integer': print dbg.search_integer_value (argv [-3])
else: print dbg.search_addr_by_value (argv [-3])
def prepareData(dataFolderPath, storagePlace, fileList, numTest,\
test='test.scp', train='train.scp'):
totlFiles = len(fileList)
if numTest > totlFiles - 1:
print 'No enough data'
sys.ex(1)
mark = [0 for _ in xrange(totlFiles)]
testFiles = []
trainFiles = []
testFilePointer = open(os.path.join(storagePlace, 'test.scp'), "w")
trainFilePointer = open(os.path.join(storagePlace, 'train.scp'), "w")
cnt = 0
while cnt < numTest:
while True:
index = random.randint(0, totlFiles-1)
if mark[index] == 0:
line = fileList[index].split('|')[1]
testFiles.append( line )
if cnt < numTest - 1:
testFilePointer.write( line + '\n' )
else:
testFilePointer.write(line)
mark[index] = 1
break
cnt += 1
firstFlag = False
for i in xrange(totlFiles):
if mark[i] == 0:
line = fileList[i].split('|')[1]
trainFiles.append( line )
if firstFlag is False:
trainFilePointer.write( line )
firstFlag = True
else:
trainFilePointer.write( '\n' + line )
testFilePointer.close()
trainFilePointer.close()
print repr(a + b), repr(a - b)
print type(a + b), type(a - b)
print a | b, abs(c)
print type(a | b), type(abs(c))
print pi * c, c * pi
print type(pi * c), type(c * pi)
#print repr(c[1]), repr(c[:-1]), a[::2], repr(c[1:2])
#print type(c[1]), type(c[:-1]), type(a[::2]), type(c[1:2]), type(a<<1)
print a == b, (a << 1) == (a >> 3), a << 1, a != b, a != a
print a ^ b, b ^ a
print "Iterator test:", tuple('<' + str(e) + '>' for e in a)
from sys import exc_info as ex
try:
a + 1
except:
print 'Caught:', ex()[1:2]
try:
a - 1
except:
print 'Caught:', ex()[1:2]
try:
a + c
except:
print 'Caught:', ex()[1:2]
try:
a - c
except:
print 'Caught:', ex()[1:2]
try:
a * b
except:
def process(pth):
print(f'\nProcessing {pth}')
save_pth = pth / 'vol_reg_stacks'
tmat_pth = pth / 'vol_transformation_matrices'
try:
save_pth.mkdir()
tmat_pth.mkdir()
except FileExistsError:
ex('Save File for reg stacks or tmats already exists. Delete and re-run.')
#Intravolume registration of the fixed volume
print('Doing intravolume registration.')
#load first stack and do a 3d gaussian blur with a sigma=1
#str needed for imread, otherwise only one frame is loaded
fixed = io.imread(str(pth/'stack0.tif')) #had gauss(), testing
#tell pystack reg that we will use a translational transformation
#there shouldn't be intra-volume rotation or shear (there might be for rod blink)
sr = StackReg(StackReg.TRANSLATION)
#register to the first slice and output the transfomation matrix without transforming
t_mats = sr.register_stack(gauss(fixed), reference='first', n_frames=1)
#remove the x shift from all the matrices - horizontal movement isn't relevant here,
#the volume should be acquired quickly enough that this isn't a problem.
t_mats[:,0,-1] = 0
fixed = sr.transform_stack(fixed, tmats=t_mats)
#save the register fixed volume in the parent directory for reference
save_name = pth.parent / 'fixed.tif'
#io.imsave(arr=img_as_uint(fixed), fname=str(save_name))
io.imsave(arr=fixed.astype('float32'), fname=str(save_name))
#get fixed out of memory - may not be worth the time?
del fixed
print(f'Intravolume registration complete. File saved at {save_name}')
#Volume registration
#switch to tmat folder because i dont know how to set the output folder to save
#the transformation mats. elastix.Execute() automatically saves
#TransformParameters.0.txt in the current directory
os.chdir(tmat_pth)
#reload fixed image with sitk so it is in the right format
fixed = sitk.ReadImage(str(save_name))
#set up for multivolume registration
parameterMap = sitk.GetDefaultParameterMap('affine')
elastixImageFilter = sitk.ElastixImageFilter()
elastixImageFilter.SetFixedImage(fixed)
elastixImageFilter.SetParameterMap(parameterMap)
#test 11-8-2019
parameterMap['Image Sampler'] = ['Full']
#parameterMap['Metric'] = ['AdvancedMeanSquares']
parameterMap['Optimiser'] = ['FullSearch']
#iterate through the files in the stacks folder
files = sorted(list(pth.glob('*.tif')), key=sort_key)
loop_starts = time.time()
for i,file in enumerate(files):
#i=0 #use first stack
#register to previous stack
if i > 1:
fixed = sitk.ReadImage(str(save_name))
elastixImageFilter.SetFixedImage(fixed)
start_time = time.time()
print(f'Processing: {file}')
#load the volume
#Do affine registration so that volume can shear to do the intravolume registration
#this code is equivalent to the lines below, but allows the export of the
#transformation matrices
#moving = sitk.ReadImage(file)
#reg_volume = sitk.Elastix(fixed, moving, "affine")
elastixImageFilter.SetMovingImage(sitk.ReadImage(str(file)))
elastixImageFilter.Execute()
reg_volume = elastixImageFilter.GetResultImage()
#can get the transform parameters, but have no idea how to save them
#maybe just through normal python file manipulation?
#transformParameterMap = elastixImageFilter.GetTransformParameterMap()
#save volume
save_name = save_pth / f'reg_{file.name}'
sitk.WriteImage(reg_volume, str(save_name))
#transformation was saved on execute, now rename.
#tmat_name = tmat_pth / f'tmat_{file.name}'
os.rename('TransformParameters.0.txt', f'tmat_{file.stem}.txt')
end_time = time.time()
print(f'{file} was processed in {(end_time - start_time):.2f}s. \
\n{((end_time - loop_starts)/60):.2f} minutes have elapsed.')
#url = str(top_link[0])
# Can replace the previous few lines with:
url = str([x.url for x in top][0])
# We'll only need the image's unique URL (i.e. after the last '/')
# I'm going to use re.split('/', url) to get the file_name.
file_name = split('/', url)[-1]
# If there's no '.jpg', '.jpeg', or '.png' at the end of url, it's either an
# album (which I don't want to deal with right now), a link to a website
# (which I probably won't ever deal with), or a .gif, so we'll ignore it.
if (file_name[-4:] not in ['.jpg', '.png'] and \
file_name[-4:] not in ['.jpeg']) or \
file_name == '' or '/' in file_name:
ex(-1)
""" Should fix this part to make it grab the next link, if possible.
That is, until it runs out of links to grab [(num_subs)*(links_per_sub)]"""
# Otherwise, the link should work, so we just download it to the wallpaper
# folder and set the desktop background to it.
# Make an opener to connect to the webpage to save the file
file_saver = urllib2.build_opener()
# Go to the page to get the image
file_page = file_saver.open(url)
# Read the picture into (binary) memory
pic = file_page.read()
score_file = open(score_file_path, "w")
score_file.truncate()
score_file.close()
#############################
# LOCATING GAME WINDOW ETC: #
#############################
#pos = agu.locateOnScreen("Images/active.png")
#if pos == None:
pos = agu.locateOnScreen("Images/unactive.png")
if pos == None:
pos = agu.locateOnScreen("Images/gameover.png")
if pos == None:
pos = agu.locateOnScreen("Images/closetoedge.png")
if pos == None:
ex("Can't find Tetris window, try moving window away from edge. Aborting.")
agu.moveTo(pos[0] - 30, pos[1] + 5)
agu.click()
pos = agu.locateOnScreen("Images/active.png")
game_region = (pos[0] - 118, pos[1] + 55, 340, 318)
initial_state = functions.Get_current_state(game_region)
# img = agu.screenshot(region=game_region)
# plt.imshow(np.array(img))
# plt.show()
# ex("saddf")
#############################
# Hyperparameters and shit: #
#############################
actions = ["nothing", "up", "down", "left", "right", "space"]
assert args.accesstoken is not None, 'Could not read cached token.'
# build image ID (name_tag) if args.imgID is not used
if args.imgID is None:
# if name and tag pair is given, join with an underscore
if args.name is not None and args.tag is not None:
args.imgID = args.name + '_' + args.tag
# if only name is given, find most recent tag
elif args.name is not None:
args.imgID = args.name + '_' + singularitypy.get_newest_img_tag(
args.name, args.accesstoken)
# if nothing given, exit with error
else:
ex('One of three options must be provided: an image ID, a container name, or a container name and tag pair.'
)
# build header and url
header = {'Authorization': 'Bearer ' + args.accesstoken}
filename = args.imgID + '.img.bz2'
url = 'https://agave.iplantc.org/singularity/v2/quay.io/biocontainers/' + filename
# get compressed file
resp = get(url, headers=header, stream=True)
assert resp.status_code == 200, 'Unable to download ' + args.imgID + '. HTTP status code ' + str(
resp.status_code)
# write file
with open(filename, 'wb') as f:
for chunk in resp:
f.write(chunk)
def Prop():
print("\033[1;31 [+]Enter 1 To see in what directory u are : \n")
print("\033[1;31 [+]Enter 2 For Installing django : \n")
print("\033[1;31 [+]Enter 3 To see what django version \n")
print("\033[1;31 [+]Enter 4 For starting a new project : \n")
print("\033[1;31 [+]Enter 5 For starting a new application : \n")
print("\033[1;31 [+]Enter 6 To apply migrates : \n")
print("\033[1;31 [+]Enter 7 To Makemigration To an app : \n")
print("\033[1;31 [+]Enter 8 To Make a super user : \n")
print("\033[1;31 [+]Enter 9 To run the Server : \n")
print("\033[1;31 [+]Enter 10 To exit the script : \n")
choose = int(input("\033[1;34m] [+]Shoose One : "))
if choose == 1 :
pwwd()
sl(6)
Prop()
if choose == 2 :
install_dj()
sl(6)
Prop()
if choose == 3 :
django_ver()
sl(6)
Prop()
if choose == 4 :
projet_nom = str(input("Choose a name for Your Project : "))
start_project(projet_nom)
sl(6)
Prop()
if choose == 5 :
print("please make sure to exit the script an to copy it into the prject file , then use it again to create apps and to run the server")
print("Make sure to migrate after creating to application ...")
app_nom = str(input("choose Your Application Name : "))
start_application(app_nom)
sl(6)
Prop()
if choose == 7 :
application_name = input("Please Enter The name of The application : ")
mkmig(application_name)
sl(6)
Prop()
if choose == 6 :
apply_migrates()
sl(6)
Prop()
if choose == 8 :
super_user()
sl(6)
Prop()
if choose == 9:
run_server()
sl(6)
Prop()
if choose == 10 :
ex(0)
d=300 nc=1 nd=1 winner="Noone" firsttime=True pa=0 pb=0 run=False play=True while True: for e in pygame.event.get(): if e.type==QUIT: ex() if e.type==KEYDOWN : if e.key == K_x: ex() if e.key == K_f: FullScreen = not FullScreen if FullScreen: screen=pygame.display.set_mode((800,600), 0, 32) else: screen=pygame.display.set_mode((800,600), 0, 32) if e.key == K_DOWN: nq=1 ns=1 elif e.key == K_UP: if q>=60:
V(0., h2+i2-j2-k2, 2.*(ij+hk), 2.*(ik-hj)), \
V(0., 2.*(ij-hk), h2-i2+j2-k2, 2.*(jk+hi)), \
V(0., 2.*(ik+hj), 2.*(jk-hi), h2-i2-j2+k2))
if __name__=='__main__':
print "===Beginning module point.py test suite==="
print "origin=",origin
a=P(1,2,3); b=P((2,3,4)); c=P([3,4,5]); d=P(V(4,5,6))
print tuple(repr(e) for e in (a,b,c,d))
a=P(1,1,2,3); b=P((1,2,3,4)); c=P([1,3,4,5]); d=P(V(1,4,5,6))
print tuple(repr(e) for e in (a,b,c,d))
b=P(1,(2,3,4)); c=P(2.0,[3,4,5]); d=P(0.0,V(4,5,6))
print tuple(repr(e) for e in (b,c,d))
from sys import exc_info as ex
try: a=P(1,2,3,4,5)
except: print 'Caught:',ex()[1:2]
try: a=P(1)
except: print 'Caught:',ex()[1:2]
print "===__init__ tests complete==="
print repr(a)
print repr(-a),repr(a+(a-b)),abs(a)
print repr(a-b),repr(a-(a-b))
print repr((a-b)-a),repr((a-b)+a)
print a==a, a==b, a!=b, a!=a
print a.p,a.infinite,a^b
print repr(~c),repr(~d),c.p,d.p
print c.infinite,d.infinite,c^d
print "===class 'P' tests complete==="
q=Q(1,2,3); i=Q(1,0,0)
print q,i,'\n',q*i,i*q
print i(q.d),q*q,q.d|q.d,'\n',q(i.d)
def log_critical(msg):
t = datetime.now().strftime('%H:%M:%S')
print '{head} {t} --> {msg}'.format(t=t,
msg=msg,
head=colored('CRITICAL:', 'red'))
ex(-2)
