def SaveShowImage(Matrix, Root=None, Suffix=None):
'''Save Image if Root is valid, otherwise show it on the screen.'''
Name = MATL.MakeRoot(Root=Root, Suffix=Suffix)
if Name is not None:
SaveImage(Matrix, Name)
else:
ShowImage(Matrix)
def ScanPoints(InputFolder,ImageExtension,ImagePrefix=None,PointsList=[(0,0)]):
Limg = MATL.getFiles(InputFolder,ImageExtension,ImagePrefix)
Lxml = MATL.getFiles(InputFolder,"xml",ImagePrefix)
#Get Angles
A=[]
for xmlf in Lxml:
A.append(GetXMLAngle(xmlf))
A.append(-180)
#Get Inensities
I=[]
for imgf in Limg:
I.append([])
for pos in PointsList:
I[-1].append(GetIntesity(imgf,pos))
I.append(I[0])
I=[list(i) for i in zip(*I)]
return A,I,Limg[0]
def runstreamline(Input1, Input2, Output):
thismodule = os.path.abspath(inspect.getfile(inspect.currentframe()))
quotInput1 = '"' + Input1 + '"'
quotInput2 = '"' + Input2 + '"'
quotOutput = '"' + Output + '"'
cmd = " ".join([
"py -2", thismodule, quotInput1, quotInput2, quotOutput,
"-Offset1 70"
])
MATL.RunProgram(cmd)
def SaveTif(Matrix, Name, resolution=None):
'''Save pixel data in matrix as 32-bit float on a tif file.'''
Name = MATL.FixName(Name, '.tif')
MyImage = Image.fromarray(np.float32(Matrix), mode="F")
if resolution:
xres, yres = resolution
kwargsdict = {
282: xres,
283: yres,
270: 'ImageJ=1.51w\nunit=micron\n',
296: 1
}
MyImage.save(Name, tiffinfo=kwargsdict)
else:
MyImage.save(Name)
def Make3DSurfaceFromHeightMapTiff(File, OFile=None, NoZeros=False):
''' Generates a ply mesh from a tiff file. Scale is extracted from tiff embedded information.
File - Tiff file with the height information
OFile[None] - Path to output ply file
NoZeros[False] - Do not generate mesh when pixel/element value is equal to zero.
'''
name, _ = os.path.splitext(File)
if OFile is None:
outfile = name + "_out.ply"
else:
outfile = MATL.FixName(OFile, "ply")
Mpix, res = MAIP.GetImageMatrix(File, Silent=True, GetTiffRes=True)
return MakeMPixMesh(Mpix,
Scale=(1 / res[0], 1 / res[1], 1.0),
Expfile=outfile,
NoZeros=NoZeros)
def test_macauley(self):
self.assertTrue(np.all(MATL.macauley(np.array([3,-3]),True)==np.array([3,0])))
self.assertTrue(np.all(MATL.macauley(np.array([3,-3]),False)==np.array([0,-3])))
def test_getMatfromCSV(self):
csvdata="1,2 ,3\n4 , 5,6\n 7,8,9"
csvfile=os.path.join(self.temppath,"mycsvfile.csv")
with open(csvfile,'w') as f:
f.write(csvdata)
self.assertTrue(np.all(MATL.getMatfromCSV(csvfile)==[[1,2,3],[4,5,6],[7,8,9]]))
def test_Timeme(self):
avgtime=MATL.Timeme(max,[4,5,6],NN=2,NNN=2,show=False)
self.assertTrue(avgtime>=0)
def test_TicToc(self):
start=MATL.Tic()
delta=MATL.Toc(start)
self.assertTrue(delta>=0)
def test_IsNew(self):
myfile_new = MATL.MakeRoot(self.temppath,"new")
open(myfile_new,'w+').close()
self.assertFalse(MATL.IsNew(self.myfile_old,myfile_new))
self.assertTrue(MATL.IsNew(myfile_new,self.myfile_old))
def test_getFiles(self):
FileNameList=['firsttest','secondtest','thirdtest']
for fn in FileNameList:
fileloc = os.path.join(self.temppath,fn+".myext")
open(fileloc,'w+').close()
self.assertTrue([os.path.splitext(os.path.basename(x))[0] for x in MATL.getFiles(self.temppath,"myext")]==FileNameList)
def SaveImageRGB(Matrix, Name, **kwargs):
'''Save pixel data in matrix as RGB on a file.'''
Name = MATL.FixName(Name, '.png')
if not type(Matrix[0, 0]) == np.ndarray:
Matrix = ConvertToRGB(Matrix, **kwargs)
Image.fromarray(Matrix, mode="RGBA").save(Name, "png")
def setUpClass(cls):
print("\n === test_MA_Tools === ")
cls.temppath = os.path.join("test","temp","")
#MATL.MakeNewDir(cls.temppath)
cls.myfile_old = MATL.MakeRoot(cls.temppath,"old")
open(cls.myfile_old,'w+').close()
def SaveImageRaw(Matrix, Name, TifRes=None, resolution=None):
'''Save pixel data in matrix as 32-bit float on a file.'''
Name = MATL.FixName(Name, '.tif')
Image.fromarray(np.float32(Matrix), mode="F").save(Name,
"TIFF",
dpi=resolution)
def MakeCSVMesh(CSVfile, verbose=True, **kwargs):
''' Generates a ply mesh from a csv file '''
if verbose: print("*Making CSV Mesh")
if verbose: print(" - Reading .csv")
npdata = MATL.getMatfromCSV(CSVfile)
return MakeMPixMesh(npdata, verbose, **kwargs)
# tiffile_unscaled = os.path.join(BaseFolder,'0kPa.tif')
# tiffile = os.path.join(BaseFolder,'0kPa_scaled.tif')
tiffile = os.path.join(BaseFolder, '0kPa.tif')
plyFile_Orig = os.path.join(BaseFolder, '0kPa_scaled.ply')
plyFile_Smooth = os.path.join(BaseFolder, '0kPa_scaled_smooth.ply')
matlabdata = r'C:\Users\Wenbin\Desktop\FIDVC-master\Matlab Code\dm2\resultsFIDVC.mat'
vtuout = os.path.join(BaseFolder, '0kPa_scaled_smooth.vtu')
# Scale Tif height map to fix spherical distorsion
# if Force or MATL.IsNew(tiffile_unscaled,tiffile):
# print("Scaling Tif file...")
# scalefactor = 1.335 #(nPBS/nH20)
# MAIP.ScaleTif(tiffile_unscaled,tiffile,scalefactor)
# Make ply from height map if heightmap is newer
if Force or MATL.IsNew(tiffile, plyFile_Orig):
print("Making 3D Surface...")
MA3D.Make3DSurfaceFromHeightMapTiff(tiffile,
OFile=plyFile_Orig,
NoZeros=True)
# Smooth ply file if input ply is new
if True or MATL.IsNew(plyFile_Orig, plyFile_Smooth):
print("Smoothing and reducing Surface...")
MACA.SmoothPly(plyFile_Orig,
plyFile_Smooth,
ScriptFileName=None,
Verbose=True,
MeshLabPath='C:\\Program Files\\VCG\\MeshLab')
test = AddDeformation(plyFile_Smooth)
"shellBC": True
},
"ME_Average": {
**casedefault, "kip": 0.184,
"load": -2E-2,
"shellBC": True
},
"ME_Uniform": {
**casedefault, "kip": 0.5,
"load": -2E-2,
"shellBC": True
},
}
destfolder = pjoin(Base_Folder, root)
MATL.MakeNewDir(destfolder)
for case in Cases:
print(root + " " + case)
casefolder = pjoin(destfolder, case)
MATL.MakeNewDir(casefolder)
febiofile = pjoin(casefolder, root + "_" + case + ".feb")
if RunModels:
FEBio.SaveFile(febiofile, **Cases[case])
print(" Running FEBio. Check logfile for details...")
MATL.RunProgram('FEBio2 "' + febiofile + '"', f_print=False)
print(" FEBio Simulation finished.")
logfile = os.path.splitext(febiofile)[0] + ".log"
with open(logfile, "r") as fp:
def SaveImage(Matrix, Name, resc=False):
'''Save pixel data in matrix as 8-bit on a file.'''
Name = MATL.FixName(Name, '.png')
if resc:
Matrix = Rescale8bit(Matrix)
Image.fromarray(np.uint8(Matrix), mode="L").save(Name, "png")
def test_RunProgram(self):
MATL.RunProgram("python -c \"print(0)\"",False)
def test_eig33s(self):
mat=np.array([[1,7,6],[7,2,5],[6,5,3]])
normdiff=np.linalg.norm(
np.sort(list(MATL.eig33s(mat[0,0],mat[1,1],mat[2,2],mat[0,1],mat[0,2],mat[1,2])))-
np.sort(np.linalg.eigvals(mat)))
self.assertTrue(normdiff<1E-12)
def test_MakeRoot(self):
mynewfile = MATL.MakeRoot(self.temppath,"TEST")
open(mynewfile,'w+').close()
self.assertTrue(os.path.isfile(os.path.join(self.temppath,"TEST")))