Python Interface.Interface类代码示例

 def setPseudoCnt(self,arglist=("1.0")):
     "Arguments: [pseudocount]\nSet the amount of pseudocounts on matricies. Default 1.0"
     try:
         Interface.setPseudoCount(self,float(arglist[0]))
     except ValueError:
         print "Invalid pseudocount. Pseudocount not set."
         return

 def __init__(self, width, height, blocksize, fullscreen=False):
     Interface.__init__(self, width, height, blocksize)
     self.flags = pygame.DOUBLEBUF | pygame.HWSURFACE
     if fullscreen:
         self.flags |= pygame.FULLSCREEN
     self.window = pygame.display.set_mode((self.width, self.height),
                                           self.flags)

def main():
    msg = WhatIsMessage()

    # The hidden prepend keyword of the text input also includes
    # double-quotes so that left whitespace is not stripped by the
    # server.
    if msg and msg.startswith("\""):
        msg = msg[1:]

    Logger("CHAT", "Console: {}: {}".format(activator.name, msg))

    console = console_find(activator)

    if msg == "exit()":
        if console:
            console_remove(activator)
            inf = Interface(activator, None)
            inf.dialog_close()

        return

    if not console:
        console = console_create(activator)

    console.push(msg)

    if not msg:
        console.show()

    def align(self, arglist):
        """Arguments: [filename[,num_of_align,[lambda[,xi[,mu[,nu,[,nuc_per_rotation, [Seq1, Seq2]]]]]]]]
aligns the computed BS or optional the BS from a gff file
filename specifies a file in gff format is you want to be aligned
num_of_align        specifies how many alignments you want. (Default 3)
lambda   Bonus factor for hit (Default 2)
xi       Penalty factor for rotation (Default 1.0)
mu       Penalty factor for average distance between sites (Default 0.5)
nu       Penalty factor for distance difference between sites (Default 1.0)
nuc_per_rotation    specifies how many nucletides there are per rotation. (Default 10.4)
Seq1,Seq2 Sequences to be aligned.
If you want to skip a argument just  write '.' for it.
If you use '.' as filename the local data are aligned."""
        try:
            [filename, num_of_align, Lambda, xi,
             mu, nu, nuc_per_rotation,Seq1,Seq2]=(arglist + ['.']*(9-len(arglist)))[:9]

            if num_of_align=='.':
                num_of_align=3
            if Lambda=='.':
                Lambda=2.0
            if xi=='.':
                xi=1.0
            if mu=='.':
                mu=0.5
            if nu=='.':
                nu=1.0
            if nuc_per_rotation=='.':
                nuc_per_rotation=10.4
            if Seq1=='.':
                Seq1=None
            if Seq2=='.':
                Seq2=None
                
            try:
                if not Interface.align(self, filename, int(num_of_align),
                                       float(Lambda), float(xi),
                                       float(mu), float(nu),
                                       float(nuc_per_rotation),Seq1,Seq2):
                    print "No alignment for a reason or an other"
            except AttributeError,val:
                if len(val.args)==1 or (len(val.args)>1 and len(val.args[1])<2):
                    print val.args[0]
                else:
                    msg,seqs=val
                    # This function is expected to be defined in subclass
                    firstSeq,secondSeq=self.selectTwoSequences(msg,seqs)
                    if not Interface.align(self, filename, int(num_of_align),
                                           float(Lambda), float(xi),
                                           float(mu), float(nu),
                                           float(nuc_per_rotation),
                                           firstSeq,secondSeq):
                        print "No alignment for a reson or an another"
        except ValueError,e:
            print "Error: unallowed arguments passed to 'align'",e

def test_dicom_download_production():
    # Example of how to download a worklist of series.
    #
    # Format worklist like this:
    #
    # SeriesInstanceUIDs:
    #   - x.y.zzz.wwwwww.u.ttt.s.aaaaaaaaaaa....
    #   - x.y.zzz.wwwwww.u.ttt.s.aaaaaaaaaab....
    #
    # Can search for "Series/Study/PatientInstanceUID", "AccessionNumber", "PatientName" or "PatientID"

    raise SkipTest

    repos = read_yaml('repos.yaml')

    source = Interface.factory('gepacs', repos)
    target = Interface.factory('deathstar', repos)

    # worklist_config = read_yaml('series_worklist.yaml')['SeriesInstanceUIDs']
    #
    # for entry in worklist_config:
#    w = source.find('study', {'AccessionNumber': 'R13851441'})[0]
    u = target.find('study', {'AccessionNumber': 'R13851441'})[0]
    #u = target.retreive(w, source)[0]
    target.copy(u, target, '/Users/derek/Desktop/%s_archive' % u.study_id.o)

def dicom_tests():

    logger = logging.getLogger(dicom_tests.__name__)

    # Test DICOM Instantiate
    from OrthancInterface import OrthancInterface
    proxy = OrthancInterface(address='http://localhost:8043', name='3dlab-dev1')
    source = DICOMInterface(proxy=proxy, name='3dlab-dev0+dcm')

    # Test DICOM Subject Query
    r = source.find('subject', {'PatientName': 'ZNE*'})[0]
    assert r.subject_id == 'ZA4VSDAUSJQA6'

    # Test DICOM Q/R/DL
    from tithonus import read_yaml
    repos = read_yaml('repos.yaml')

    source = Interface.factory('3dlab-dev0+dcm', repos)
    target = Interface.factory('3dlab-dev1', repos)

    w = source.find('series', {'SeriesInstanceUID': '1.2.840.113654.2.55.4303894980888172655039251025765147023'})[0]
    u = target.retrieve(w, source)[0]
    target.copy(u, target, 'nlst_tmp_archive')
    assert os.path.getsize('nlst_tmp_archive.zip') == 176070
    os.remove('nlst_tmp_archive.zip')

    def YoutubeLinkDownload(self):
        txt, ok = QtGui.QInputDialog.getText(
            self, "YouTube Link", "YTube Link:", QtGui.QLineEdit.Normal, "", QtCore.Qt.FramelessWindowHint
        )
        if ok == True:
            if txt.startsWith("https://www.youtube.com"):
                key = self.freeKey()
                if key == -1:
                    obj = Interface(self.PARTS)
                else:
                    obj = self.dLoads[key]
                    obj.PARTS = self.PARTS
                    obj.clear()
                    del self.dLoads[key]

                thread.start_new_thread(obj.start_Download, (txt, self.wMutex))
                self.dLoads[self.links] = obj
                self.links = self.links + 1
            else:
                msg = QtGui.QMessageBox(
                    QtGui.QMessageBox.Warning,
                    "Oops.",
                    "Not a valid YTube Url ",
                    QtGui.QMessageBox.Ok,
                    self,
                    QtCore.Qt.FramelessWindowHint,
                )
                msg.show()

 def removeMatrix(self, arglist):
     "Arguments: Matrixnumber\nremoves a matrix"
     try:
         index=string.atoi(arglist[0])
         Interface.removeMatrix(self, index)
     except ValueError:
         print arglist[0],"is not a number"

    def fetchAndSaveUrl(self, url="", bit=1):
        ok = True
        if len(url) == 0:
            url, ok = QtGui.QInputDialog.getText(
                self, "Link", "Download Link:", QtGui.QLineEdit.Normal, "", QtCore.Qt.FramelessWindowHint
            )
        if ok == True:
            key = self.freeKey()
            if key == -1:
                obj = Interface(self.PARTS)
                key = self.links
                self.links = self.links + 1
            else:
                obj = self.dLoads[key]
                obj.PARTS = self.PARTS
                obj.clear()
                del self.dLoads[key]

            thread.start_new_thread(obj.start_Download, (url, self.wMutex, bit))
            self.dLoads[key] = obj
        else:
            msg = QtGui.QMessageBox(
                QtGui.QMessageBox.Warning,
                "Oops.",
                "Not a valid Url ",
                QtGui.QMessageBox.Ok,
                self,
                QtCore.Qt.FramelessWindowHint,
            )
            msg.show()

class Program:
	"""
	General program template
	 - init function for program component initialization
	 - main loop
	 	* check events -> handle (event)
	 	* update
	"""

	def __init__(self):
		"""
		init function
		"""

		self.interface = Interface()
		self.engine = Engine()
		self.run()


	def run(self):
		"""
		main loop
		"""

		while True:
			self.check_events()
			self.update()


	def check_events(self):
		"""
		pygame event handling (edit this for more events)
		"""

		for event in pygame.event.get():
			if event.type == pygame.QUIT:
				pygame.quit()
				sys.exit()
			if event.type == pygame.MOUSEBUTTONDOWN:
				mousex, mousey = event.pos
				response = self.interface.click(mousex,mousey)
				self.handle(response)


	def handle(self,response):
		"""
		handle responses to events
		"""

		self.engine.send(response)
		

	def update(self):
		"""
		update state of program components
		"""

		self.engine.update()
		self.interface.update(self.engine.get_updates())

 def addSequence(self, arglist):
     "Arguments: filelist\nreads sequences from files"
     for filestring in arglist:
         filenames=glob(filestring)
         if filenames:
             Interface.addSequence(self, filenames)
         else:
             raise CommandError("file not found:"+filestring)

    def getTFBSpvalue(self, arglist):
        """Arguments: [pvalue]
computes the scores of all matrices and all sequences. Report scores
better than given p-value.
The default value for pvalue is 1e-6"""
        cutoff=1e-6
        try:
            if(len(arglist)>0):
                cutoff= string.atof(arglist[0])
            Interface.getTFBSpvalue(self, cutoff)
        except ValueError:
            print "getTFBSpvalue requires an numeric argument!"

    def getTFBSabsolute(self, arglist):
        """Arguments: [cutoff]
computes the scores of all matrices and all sequences which are
better than cutoff.
The default value for cutoff is 9.0"""
        cutoff=9.0
        try:
            if(len(arglist)>0):
                cutoff= string.atof(arglist[0])
            Interface.getTFBSAbsolute(self, cutoff)
        except ValueError:
            print "getTFBSabsolute requires an numeric argument!"

    def getTFBS(self, arglist):
        """Arguments: [bound]
computes the scores of all matrices and all sequences which are
better than log2(bound) + maxscore. maxscore is the highest reachable
score of the actual matrix with respect to the background
The default value for bound is 0.1 i.e. ~3.3 below the maximum score."""
        bound=0.1
        try:
            if(len(arglist)>0):
                bound= string.atof(arglist[0])
            Interface.getTFBS(self, bound)
        except ValueError:
            print "getTFBS requires an numeric argument!"

def test_dicom_download_dev():

    # Test DICOM Download (also in DICOMInterface)

    repos = read_yaml('repos.yaml')

    source = Interface.factory('3dlab-dev0+dcm', repos)
    target = Interface.factory('3dlab-dev1', repos)

    w = source.find('series', {'SeriesInstanceUID': '1.2.840.113654.2.55.4303894980888172655039251025765147023'})
    u = target.retrieve(w[0], source)
    target.copy(u[0], target, 'nlst_tmp_archive')
    assert os.path.getsize('nlst_tmp_archive.zip') == 176070
    os.remove('nlst_tmp_archive.zip')