def run_scipion_qc(movie_file):
manager = Manager()
project = manager.loadProject(PROJECT)
path, pattern = os.path.split(movie_file)
add_movies = project.newProtocol(
ProtImportMovies,
filesPath=path,
filesPattern=pattern,
voltage=VOLTAGE,
samplingRate=SAMPLING_RATE,
)
project.launchProtocol(add_movies, wait=True)
align_movies = project.newProtocol(
ProtMovieAlignment,
inputMovies=add_movies.outputMovies,
)
project.launchProtocol(align_movies, wait=True)
find_ctf = project.newProtocol(
ProtCTFFind,
inputMicrographs=align_movies.outputMicrographs,
)
project.launchProtocol(find_ctf, wait=False)
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
btn = HotButton(self,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
try:
project = self.manager.loadProject(p.getName(), chdir=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
frame = self.createProjectLabel(parent, p, color=colors[i % 2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def __init__(self):
projName = self.__class__.__name__
manager = Manager()
if manager.hasProject(projName):
self.project = manager.loadProject(projName)
else:
self.project = manager.createProject(projName)
# Use graph view as default
settings = self.project.getSettings()
settings.setRunsView(1) # graph view
settings.write()
self.loadWorkflow()
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize, family=fontName, weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize, family=fontName, weight='bold')
self.manager = Manager()
btn = HotButton(self, text=Message.LABEL_CREATE_PROJECT, font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
try:
project = self.manager.loadProject(p.getName(), chdir=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
frame = self.createProjectLabel(parent, p, color=colors[i%2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
except Exception, ex:
print "ERROR loading project: %s" % p.getName()
print ex
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def _writeSubset(self, subset):
""" Generated the output of this subset. """
newSubsetName = 'outputParticles_%03d' % self._counter
self.info("Creating new subset: %s" % newSubsetName)
subset.write()
self._defineOutputs(**{newSubsetName: subset})
self._defineTransformRelation(self.inputParticles, subset)
# The following is required to commit the changes to the database
self._store(subset)
subset.close()
from pyworkflow.manager import Manager
manager = Manager()
project = manager.loadProject(self.getProject().getName())
input2D = self.input2dProtocol.get()
copyProt = project.copyProtocol(project.getProtocol(input2D.getObjId()))
copyProt.inputParticles.set(project.getProtocol(self.getObjId()))
copyProt.inputParticles.setExtended(newSubsetName)
project.scheduleProtocol(copyProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(copyProt.getObjId())
argc = len(sys.argv)
if argc < 3 or argc > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
protId = sys.argv[2]
manager = Manager()
if not manager.hasProject(projName):
usage("Unexistent project: %s" % pwutils.red(projName))
project = manager.loadProject(projName)
prot = project.getProtocol(protId)
if prot is None:
usage("Unexistent protocol: %s" % protId)
outputParticles = getattr(prot, 'outputParticles', None)
if outputParticles is None:
usage("Protocol does not have 'outputParticles'")
realDims = outputParticles.getDimensions()
print "Real dimensions: ", realDims
print "DB dimensions: ", outputParticles.getDim()
tempSpace = "loading-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(os.environ['SCIPION_USER_DATA'],
'tmp', tempSpace)
projectsDir = os.path.join(customUserData, 'projects')
pwutils.makePath(projectsDir)
print "Loading projects from:\n", projectsDir
projName = os.path.basename(pathToProj)
pwutils.createAbsLink(pathToProj, os.path.join(projectsDir, projName))
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
proj = manager.loadProject(projName)
projPath = manager.getProjectPath(projName)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
print "Error: ", ex
ProjectWindow.close(self, e)
projWindow = EditorProjectWindow(projPath)
projWindow.show()
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize, family=fontName, weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize, family=fontName, weight='bold')
self.manager = Manager()
btn = HotButton(self, text=Message.LABEL_CREATE_PROJECT, font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
project = self.manager.loadProject(p.getName(), chdir=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
frame = self.createProjectLabel(parent, p, color=colors[i%2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def createProjectLabel(self, parent, projInfo, color):
frame = tk.Frame(parent, bg=color)
label = tk.Label(frame, text=projInfo.projName, anchor='nw', bg=color,
justify=tk.LEFT, font=self.projNameFont, cursor='hand1', width=50)
label.grid(row=0, column=0, padx=2, pady=2, sticky='nw')
label.bind('<Button-1>', lambda e: self.openProject(projInfo.projName))
dateMsg = '%s%s %s%s' % (Message.LABEL_MODIFIED, prettyDate(projInfo.mTime),
Message.LABEL_CREATED, prettyTime(projInfo.cTime, time=False))
dateLabel = tk.Label(frame, text=dateMsg, font=self.projDateFont, bg=color)
dateLabel.grid(row=1, column=0, sticky='nw')
delLabel = tk.Label(frame, text=Message.LABEL_DELETE_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
delLabel.grid(row=1, column=1, padx=10)
delLabel.bind('<Button-1>', lambda e: self.deleteProject(projInfo.projName))
mvLabel = tk.Label(frame, text=Message.LABEL_RENAME_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
mvLabel.grid(row=1, column=2)
mvLabel.bind('<Button-1>', lambda e: self.renameProject(projInfo.projName))
return frame
def createNewProject(self, projName, projLocation):
self.manager.createProject(projName, location=projLocation)
self.createProjectList(self.text)
self.openProject(projName)
def _onCreateProject(self, e=None):
projWindow = ProjectCreateWindow("Create project", self)
projWindow.show()
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([os.environ['SCIPION_PYTHON'], script, projName])
def deleteProject(self, projName):
if askYesNo(Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT, self.root):
self.manager.deleteProject(projName)
self.createProjectList(self.text)
def renameProject(self, projName):
newName = askString("Rename project %s" % projName, "Enter new name:", self.root)
if not newName or newName == projName:
return
if self.manager.hasProject(newName):
showError("Rename cancelled",
"Project name already exists: %s" % newName, self.root)
return
self.manager.renameProject(projName, newName)
self.createProjectList(self.text)
parser.add_argument('project', type=str, help='Scipion project')
parser.add_argument('directory', type=str, help='Directory to monitor')
args = parser.parse_args()
PROJECT = args.project
VOLTAGE = args.voltage
SAMPLING_RATE = args.sampling_rate
PROCESSES = args.processes
POOL = Pool(processes=PROCESSES)
# Create or load project
manager = Manager()
if manager.hasProject(PROJECT):
project = manager.loadProject(PROJECT)
else:
project = manager.createProject(PROJECT)
# First, start up watchdog
event_handler = MyEventHandler()
observer = Observer()
observer.schedule(event_handler, path=args.directory, recursive=False)
observer.start()
print('Watchdog started; to exit, press Control-C')
# Second, run all existing files
for f in os.listdir(args.directory):
try:
ext = os.path.splitext(f)[1].split('.')[1]
if ext in ACCEPTED_EXTENSIONS:
