def getJavaIJappCmd(memory, appName, args, batchMode=False):
'''Launch an Java application based on ImageJ '''
from protlib_filesystem import getXmippPath
if len(memory) == 0:
memory = "2g"
print "No memory size provided. Using default: " + memory
imagej_home = getXmippPath("external", "imagej")
lib = getXmippPath("lib")
javaLib = getXmippPath('java', 'lib')
plugins_dir = os.path.join(imagej_home, "plugins")
arch = getArchitecture()
cmd = "java -Xmx%(memory)s -d%(arch)s -Djava.library.path=%(lib)s -Dplugins.dir=%(plugins_dir)s -cp %(imagej_home)s/*:%(javaLib)s/* %(appName)s %(args)s" % locals()
if batchMode:
cmd += " &"
return cmd
def getXmippLabels():
''' Parse the labels definition from the 'libraries/data/metadata_label.h' file '''
labelHeader = getXmippPath(os.path.join('libraries', 'data', 'metadata_label.h'))
f = open(labelHeader)
labels = []
comments = {}
labelsPrefixes = ['MDL_', 'RLN_', 'BSOFT_']
for line in f:
line = line.strip()
for prefix in labelsPrefixes:
if line.startswith(prefix) and '///<' in line:
parts = line.split('///<')
mdl = parts[0].strip()[:-1] # remove last comma
comm = parts[1].strip()
comments[mdl] = comm
if line.startswith('MDL::addLabel(' + prefix):
l = line.find('(')
r = line.find(')')
parts = line[l + 1:r].split(',')
label = {}
label['name'] = parts[2].replace('"', '').strip()
label['type'] = parts[1].strip()
label['enum'] = parts[0].strip()
label['comment'] = comments.get(label['enum'], "")
labels.append(label)
return labels
def createPanels(self):
root = self.master
root.columnconfigure(0, minsize=100, weight=1)
root.columnconfigure(1, minsize=360, weight=4)
root.rowconfigure(0, weight=1)
registerCommonFonts()
#left panel
bgColor = 'white'
leftFrame = tk.Frame(root, bg=bgColor)
leftFrame.columnconfigure(0, weight=1)
leftFrame.rowconfigure(0, minsize=100)
imgPath = getXmippPath('resources', 'xmipp_logo.gif')
self.img = tk.PhotoImage(file=imgPath)
tk.Label(leftFrame, image=self.img, bg=bgColor).grid(column=0, row=0, sticky='we')
tk.Label(leftFrame, text='Xmipp '+ getXmippVersion(), font=Fonts['button'], bg=bgColor).grid(column=0, row=1, sticky='we')
# TODO: insert revision extracting it from git repository
# tk.Label(leftFrame, text='r12.4.3.11834', bg=bgColor).grid(column=0, row=2, sticky='we')
leftFrame.grid(column=0, row=0, sticky='nsew', padx=5, pady=5, rowspan=2)
self.grid(column=1, row=0, sticky='nsew', padx=5, pady=5)
self.nb = ttk.Notebook(self.master)
self.nb.grid(row=0, column=1, sticky='nsew', padx=5, pady=5)
self.addTab("About", "README")
self.addTab("Authors", "AUTHORS", getAuthorLine)
self.addTab("Software", "SOFTWARE")
self.addTab("License", "COPYING")
self.btn = XmippButton(self.master, text='Close')
self.btn.grid(row=1, column=1, sticky='se', padx=5, pady=5)
self.btn.config(command=self.close)
self.btn.bind('<Return>', func=self.close)
self.btn.focus_set()
def createImageButton(parent, text, image, cmd):
try:
helpImage = PhotoImage(file = getXmippPath(os.path.join("resources", image)))
btn = Button(parent, image=helpImage, command=cmd, bd=0)
btn.image = helpImage;
except TclError:
btn = Button(parent, text=text, bg="#a7dce1", activebackground="#72b9bf",
command=cmd)
return btn
def getImageJPluginCmd(memory, macro, args, batchMode=False):
from protlib_filesystem import getXmippPath
if len(memory) == 0:
memory = "1g"
print "No memory size provided. Using default: " + memory
imagej_home = getXmippPath("external/imagej")
plugins_dir = os.path.join(imagej_home, "plugins")
macro = os.path.join(imagej_home, "macros", macro)
imagej_jar = os.path.join(imagej_home, "ij.jar")
cmd = """ java -Xmx%s -Dplugins.dir=%s -jar %s -macro %s "%s" """ % (memory, plugins_dir, imagej_jar, macro, args)
if batchMode:
cmd += " &"
return cmd
def run(self):
fn = self.getParam("-i")
from os.path import splitext
[fnBase, ext] = splitext(fn)
if ext != ".cpp":
reportError(fn + " is not a .cpp file")
command = "g++ "
if self.checkParam("--debug"):
command += "-g -pg"
xmippDir = getXmippPath()
if xmippDir == "":
reportError("$XMIPP_HOME is not set in the environment")
scipionDir = os.environ["SCIPION_HOME"]
command += (
" -o "
+ fnBase
+ " "
+ fn
+ " -O -D_LINUX "
+ "-L"
+ xmippDir
+ "/lib "
+ "-I"
+ xmippDir
+ "/libraries "
+ "-I"
+ xmippDir
+ " "
+ "-lXmippClassif -lXmippData -lXmippInterface -lXmippRecons -lXmippDimred -lXmippBilib -lfftw3 -lfftw3_threads -lsqlite3 -ltiff -ljpeg"
)
command += (
" -I"
+ xmippDir
+ "/external/python/Python-2.7.2/Include -I"
+ xmippDir
+ "/external/python/Python-2.7.2 -L"
+ xmippDir
+ "/external/python/Python-2.7.2 -lpython2.7 -I"
+ xmippDir
+ "/lib/python2.7/site-packages/numpy/core/include"
+ " -I"
+ xmippDir
+ "/external"
+ " -I"
+ scipionDir
+ "/software/include -L"
+ scipionDir
+ "/software/lib"
)
os.system(command)
def addTab(self, text, file, processLine=None):
tab = tk.Frame(self.nb)
self.nb.add(tab, text=text)
self.tabs[text] = tab
txt = TaggedText(tab, width=60, height=20, bg='lightgray');
txt.frame.grid(column=0, row=0, sticky='nsew', padx=10, pady=10)
f = open(getXmippPath(file))
for line in f:
if processLine:
line = processLine(line)
if line:
txt.addLine(line)
f.close()
txt.setReadOnly(True)
return txt
def setUp(self):
"""This function performs all the setup stuff.
"""
os.environ['PROTOCOL_SCRIPT'] = sys.argv[0]
#run this at xmipp level
# Asume 'xmipp' and 'testXmipp' are at the same level
curdir = os.path.dirname(getXmippPath())
self.ProjectDir = join(curdir, 'testXmipp/input/Protocol_Projection_Matching')
self.WorkingDir = 'ProjMatch/new20'
self.goldWorkingDir = 'ProjMatch/goldStandard'
self.path = join(self.ProjectDir,self.WorkingDir)
tmpPath = join(self.path, 'tmp')
mkpath(tmpPath, 0777, True)
os.chdir(self.ProjectDir)
print "Changed directory to", self.ProjectDir
self.log = XmippLog(join(tmpPath, 'projmatch.log'))
self.src = 'ProjMatch/goldStandard/'
self.dst = 'ProjMatch/new20/'
def getXmippLabelsName():
''' Parse the labels name from the 'libraries/data/metadata_label.h' file '''
labelHeader = getXmippPath(os.path.join('libraries', 'data', 'metadata_label.h'))
f = open(labelHeader)
labels = []
comments = {}
for line in f:
line = line.strip()
if line.startswith('MDL_') and '///<' in line:
parts = line.split('///<')
mdl = parts[0].strip()[:-1] # remove last comma
comm = parts[1].strip()
comments[mdl] = comm
if line.startswith('MDL::addLabel(MDL_'):
l = line.find('(')
r = line.find(')')
parts = line[l + 1:r].split(',')
labels.append(parts[2].replace('"', '').strip())
return labels
def validate(self):
errors = []
fnShAlignment=getXmippPath('lib/python2.7/site-packages/sh_alignment')
if not os.path.exists(fnShAlignment) and self.AlignmentMethod=="Fast Fourier":
errors.append("Fast Fourier can only be used if Xmipp has been installed with FRM support")
return errors
class TestEMX(unittest.TestCase):
testsPath = getXmippPath("resources", "test")
def setUp(self):
"""This function performs all the setup stuff.
"""
os.chdir(self.testsPath)
def test_00emxMicrograph(self):
""" Create micrograph and play a little with it
"""
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
#reference
dictPrimaryKeys = collections.OrderedDict([('fileName', 'mic'),
('index', 1)])
dictAttributes = collections.OrderedDict([('acceleratingVoltage', 100),
('defocusU', 1000.0),
('pixelSpacing__X', 5.6),
('pixelSpacing__Y', 5.7)])
self.assertEqual(m1.dictPrimaryKeys, dictPrimaryKeys)
self.assertEqual(m1.dictAttributes, dictAttributes)
def test_10emxParticle(self):
""" Create a particle and play a little with it
"""
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
p1 = EmxParticle('part', 1)
p1.set('defocusU', 1000.10)
p1.set('pixelSpacing__X', 5.66)
p1.set('pixelSpacing__Y', 5.77)
p1.setMicrograph(m1)
#reference
dictPrimaryKeys = collections.OrderedDict([('fileName', 'part'),
('index', 1)])
dictAttributes = collections.OrderedDict([('defocusU', 1000.1),
('pixelSpacing__X', 5.66),
('pixelSpacing__Y', 5.77)])
dictForeignKeys = collections.OrderedDict([('fileName', 'mic'),
('index', 1)])
#dictForeignKeys
self.assertEqual(p1.dictPrimaryKeys, dictPrimaryKeys)
self.assertEqual(p1.dictAttributes, dictAttributes)
self.assertEqual(p1.dictForeignKeys[MICROGRAPH].dictPrimaryKeys,
dictForeignKeys)
def test_20clear(self):
"""Test clear function
"""
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.27)
m1.clear()
m2 = EmxMicrograph('mic', 1)
m2.set('activeFlag', None)
self.assertEqual(m1, m2)
self.assertFalse(m1.strongEq(m2))
def test_30read(self):
#fileName = "massive_million.xml"
#fileName = "massive_100000.xml"
fileName = join(self.testsPath, 'EMX/EMXread.emx')
emxData = EmxData()
emxData.read(fileName)
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100.)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
m2 = EmxMicrograph('mic', 2)
m2.set('acceleratingVoltage', 200.)
m2.set('defocusUAngle', 135.)
p1 = EmxParticle('parti', 1)
p1.set('boxSize__X', 11)
p1.set('boxSize__Y', 33)
p1.set('defocusU', 1000.)
p1.set('pixelSpacing__X', 55.6)
p1.set('pixelSpacing__Y', 55.7)
p1.set('transformationMatrix__t11', 11.1)
p1.set('transformationMatrix__t12', 12.1)
p1.set('transformationMatrix__t13', 13.1)
p1.set('transformationMatrix__t14', 14.1)
p1.set('transformationMatrix__t21', 21.1)
p1.set('transformationMatrix__t24', 24.1)
p1.set('transformationMatrix__t31', 31.1)
p1.set('transformationMatrix__t32', 32.1)
p1.set('transformationMatrix__t33', 33.1)
p1.set('transformationMatrix__t34', 34.1)
p1.setMicrograph(m1)
self.assertTrue(emxData.objLists[MICROGRAPH][0].strongEq(m1))
self.assertTrue(emxData.objLists[MICROGRAPH][1].strongEq(m2))
self.assertTrue(emxData.objLists[PARTICLE][0].strongEq(p1))
def test_31_firstObject(self):
#fileName = "massive_million.xml"
#fileName = "massive_100000.xml"
fileName = join(self.testsPath, 'EMX/EMXread.emx')
emxData = EmxData()
mic = emxData.readFirstObject(MICROGRAPH, fileName)
m1 = EmxMicrograph('mic', 1)
self.assertEqual(mic, m1, "first micrograph differ from expected")
particle = emxData.readFirstObject(PARTICLE, fileName)
p1 = EmxParticle('parti', 1)
self.assertEqual(particle, p1, "first particle differ from expected")
def test_35size(self):
emxData = EmxData()
p1 = EmxParticle('part', 1)
p1.set('defocusU', 1000.10)
p1.set('pixelSpacing__X', 5.66)
p1.set('pixelSpacing__Y', 5.77)
emxData.addObject(p1)
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
for i in range(1, 10):
m1.set('index', i)
emxData.addObject(m1)
self.assertEqual(emxData.size(), 10)
def test_40write(self):
fileName = join(self.testsPath, 'EMX/EMXwrite.emx')
emxData = EmxData()
for i in range(1, 3):
m1 = EmxMicrograph('mic', i)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
emxData.addObject(m1)
p1 = EmxParticle('part', 1)
p1.set('defocusU', 1000.10)
p1.set('pixelSpacing__X', 5.66)
p1.set('pixelSpacing__Y', 5.77)
p1.set('transformationMatrix__t11', 11)
p1.set('transformationMatrix__t12', 12)
p1.set('transformationMatrix__t13', 13)
p1.set('transformationMatrix__t14', 14)
p1.set('transformationMatrix__t21', 21)
p1.set('transformationMatrix__t22', 22)
p1.set('transformationMatrix__t23', 23)
p1.set('transformationMatrix__t24', 24)
p1.set('transformationMatrix__t31', 31)
p1.set('transformationMatrix__t32', 32)
p1.set('transformationMatrix__t33', 33)
p1.set('transformationMatrix__t34', 34)
p1.setMicrograph(m1)
#TODO: check the following line
#p1.addForeignKey(MICROGRAPH,m1)
emxData.addObject(p1)
fileName2 = os.path.join('/tmp', 'EMXwrite.emx')
emxData.write(fileName2)
#print "kdiff3", fileName,fileName2
self.assertTrue(filecmp.cmp(fileName, fileName2))
if os.path.exists(fileName2):
os.remove(fileName2)
def test_50MasiveReadWrite(self):
"""This is not really a test
but an auxiliary function
"""
fileName2 = join(self.testsPath, 'EMX/EMXMasiveWrite.emx')
emxDataW = EmxData()
emxDataR = EmxData()
numberMic = 3
numberPartPerMic = 2
# numberMic=100
# numberPartPerMic = 1000
for i in range(1, numberMic):
m1 = EmxMicrograph('mic', i)
m1.set('acceleratingVoltage', 100)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
emxDataW.addObject(m1)
for p in range(1, numberPartPerMic):
p1 = EmxParticle('part', p)
p1.set('defocusU', 1000.10)
p1.set('pixelSpacing__X', 5.66)
p1.set('pixelSpacing__Y', 5.77)
p1.setMicrograph(m1)
emxDataW.addObject(p1)
fn = os.path.join('/tmp', 'EMXMasiveWrite.emx')
fn2 = fn.replace('.emx', '2.emx')
emxDataW.write(fn)
emxDataR.read(fn)
emxDataR.write(fn2)
self.assertTrue(filecmp.cmp(fn, fn2))
#print "kdiff3", fn,fn+"2"
if os.path.exists(fn):
os.remove(fn)
if os.path.exists(fn2):
os.remove(fn2)
def test_60iterate(self):
#fileName = "massive_million.xml"
#fileName = "massive_100000.xml"
fileName = join(self.testsPath, 'EMX/EMXread.emx')
emxData = EmxData()
emxData.read(fileName)
_list = []
m1 = EmxMicrograph('mic', 1)
m1.set('acceleratingVoltage', 100.)
m1.set('defocusU', 1000.)
m1.set('pixelSpacing__X', 5.6)
m1.set('pixelSpacing__Y', 5.7)
_list.append(m1)
m2 = EmxMicrograph('mic', 2)
m2.set('acceleratingVoltage', 200.)
m2.set('defocusUAngle', 135.)
_list.append(m2)
p1 = EmxParticle('parti', 1)
p1.set('boxSize__X', 11)
p1.set('boxSize__Y', 33)
p1.set('defocusU', 1000.)
p1.set('pixelSpacing__X', 55.6)
p1.set('pixelSpacing__Y', 55.7)
p1.set('transformationMatrix__t11', 11.1)
p1.set('transformationMatrix__t12', 12.1)
p1.set('transformationMatrix__t13', 13.1)
p1.set('transformationMatrix__t14', 14.1)
p1.set('transformationMatrix__t21', 21.1)
p1.set('transformationMatrix__t24', 24.1)
p1.set('transformationMatrix__t31', 31.1)
p1.set('transformationMatrix__t32', 32.1)
p1.set('transformationMatrix__t33', 33.1)
p1.set('transformationMatrix__t34', 34.1)
def test_70schema(self):
xmlFile = join(self.testsPath, 'EMX/EMXwrite.emx')
(code, _out, _err) = validateSchema(xmlFile)
self.assertEqual(code, 0)
xmlFile = join(self.testsPath, 'EMX/EMXwrite_badly_formed.emx')
try:
validateSchema(xmlFile)
except ValidateError, v:
print "EXCEPTION TESTING STARTS HERE: an Error message should appear. It is OK disregard it."
print "Validate Error"
print v.getCode(), v.getMessage()
print "EXCEPTION TESTING ENDS HERE."
except Exception, e:
print "ERROR; we should have never arrive here:", e
self.assertEqual(1, 0)
def runJavaJar(memory, jarName, args, batchMode=True):
from protlib_filesystem import getXmippPath
jarPath = getXmippPath(jarName)
runJavaIJapp(memory, '-jar %s' % jarPath, args, batchMode)
def getProgramsDbName():
return os.path.join(getXmippPath(), '.xmipp_programs.sqlite')
def getXmippPrograms():
'''Return the list of Xmipp's programs, taken from from bin/ folder'''
from glob import glob
programs = [os.path.basename(p) for p in glob(os.path.join(getXmippPath(), 'bin', 'xmipp_*'))]
programs.sort()
return programs
def run(self):
volfile = self.getParam("-i")
if not xmippExists(volfile):
print "ERROR: File " + volfile + "does not exist\n"
sys.exit(1)
mode = self.getParam("-m")
angulardistfile = self.getParam("-a")
if angulardistfile == "none":
angulardistfile = None
else:
if not exists(angulardistfile): # either file does not exists or has a blockname
if not (existsBlockInMetaDataFile(angulardistfile)): # check blockname
print "ERROR: File " + angulardistfile + "does not exist or block is missing\n"
sys.exit(1)
spheres_color = self.getParam("-a", 1)
spheres_distance = self.getParam("-a", 2)
spheres_maxradius = self.getParam("-a", 3)
isprojector = mode == "projector"
if isprojector:
size = self.getParam("-m", 1)
padding_factor = self.getDoubleParam("-m", 2)
max_freq = self.getDoubleParam("-m", 3)
spline_degree_str = self.getParam("-m", 4)
if spline_degree_str.lower() == "NEAREST".lower():
spline_degree = NEAREST
elif spline_degree_str.lower() == "LINEAR".lower():
spline_degree = LINEAR
elif spline_degree_str.lower() == "BSPLINE2".lower():
spline_degree = BSPLINE2
elif spline_degree_str.lower() == "BSPLINE3".lower():
spline_degree = BSPLINE3
elif spline_degree_str.lower() == "BSPLINE4".lower():
spline_degree = BSPLINE4
# print spline_degree
voxelSize = self.getParam("-s")
if voxelSize == "none":
voxelSize = None
port = self.getFreePort()
if not port:
print "ERROR: Port is not available\n"
sys.exit(1)
chimera = which("chimera")
if chimera is None:
print "ERROR: Chimera is not available\n"
sys.exit(1)
serverfile = getXmippPath("libraries/bindings/chimera/xmipp_chimera_server.py")
# command = "export XMIPP_CHIMERA_PORT=%d; chimera %s &" % (port,serverfile)
command = "chimera --script '%s %s' &" % (serverfile, port)
system(command)
if isprojector:
XmippProjectionExplorer(
volfile,
port,
[angulardistfile, spheres_color, spheres_distance, spheres_maxradius],
size,
padding_factor,
max_freq,
spline_degree,
voxelSize,
)
# print 'created projection explorer'
elif mode == "viewer":
client = XmippChimeraClient(
volfile, port, [angulardistfile, spheres_color, spheres_distance, spheres_maxradius], voxelSize
)