コード例 #1
0
ファイル: skeletonnode.py プロジェクト: anilkunwar/OOF2
        def nearestNode(self, point):
            where = self.properTile(point)

            count = 0  # No. of tile-bands containing nodes
            iter = 1   # No. of tile-bands having been looked at
            nodes = self[where][:]
            while count < 2:   
                # Initial check
                if iter==1:
                    if nodes: count += 1
                # Additional band of tiles
                addition = self.nextBand(
                    ll=primitives.iPoint(where.x-iter, where.y-iter),
                    ur=primitives.iPoint(where.x+iter, where.y+iter))
                if addition:
                    nodes += addition
                    count += 1
                else:
                    if count==1:
                        break  # No need to look for another band
                # Ready for the next round
                iter += 1

            # Find the nearest node among collected nodes
            nearest = nodes[0]
            mindist = (nearest.position() - point)**2
            for node in nodes[1:]:
                dd = (node.position() - point)**2
                if dd < mindist:
                    mindist = dd
                    nearest = node
            return nearest
コード例 #2
0
        def nearestNode(self, point):
            where = self.properTile(point)

            count = 0  # No. of tile-bands containing nodes
            iter = 1  # No. of tile-bands having been looked at
            nodes = self[where][:]
            while count < 2:
                # Initial check
                if iter == 1:
                    if nodes: count += 1
                # Additional band of tiles
                addition = self.nextBand(
                    ll=primitives.iPoint(where.x - iter, where.y - iter),
                    ur=primitives.iPoint(where.x + iter, where.y + iter))
                if addition:
                    nodes += addition
                    count += 1
                else:
                    if count == 1:
                        break  # No need to look for another band
                # Ready for the next round
                iter += 1

            # Find the nearest node among collected nodes
            nearest = nodes[0]
            mindist = (nearest.position() - point)**2
            for node in nodes[1:]:
                dd = (node.position() - point)**2
                if dd < mindist:
                    mindist = dd
                    nearest = node
            return nearest
コード例 #3
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 def __init__(self, array):
     prog = progress.getProgress("CategoryMap", progress.DEFINITE)
     n = 0
     # array is a list of lists of Ints, which are pixel categories
     self.pxls = {}  # list of pixels, keyed by category
     # TODO OPT: use iterator?
     for j in range(len(array)):
         sublist = array[j]
         for i in range(len(sublist)):
             if config.dimension() == 2:
                 where = primitives.iPoint(i, j)
                 category = sublist[i]
                 try:
                     self.pxls[category].append(where)
                 except KeyError:
                     self.pxls[category] = [where]
             elif config.dimension() == 3:
                 subsublist = sublist[i]
                 total = len(array) * len(sublist) * len(subsublist)
                 for k in range(len(subsublist)):
                     where = primitives.iPoint(i, j, k)
                     category = subsublist[k]
                     try:
                         self.pxls[category].append(where)
                     except KeyError:
                         self.pxls[category] = [where]
                     prog.setMessage("Got category for %d/%d voxels" %
                                     (n, total))
                     prog.setFraction(float(n) / total)
                     n = n + 1
     prog.finish()
コード例 #4
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 def queryPixel(self, menuitem, x, y, z=0):  # menu callback
     self.timestamp.increment()
     if config.dimension() == 2:
         self.point = primitives.iPoint(x, y)
     elif config.dimension() == 3:
         self.point = primitives.iPoint(x, y, z)
     switchboard.notify(self)  # caught by GUI toolbox
     switchboard.notify('redraw')
コード例 #5
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 def coords(self):
     if config.dimension() == 2:
         for j in range(self._isize[1]):
             for i in range(self._isize[0]):
                 yield primitives.iPoint(i, j)
     if config.dimension() == 3:
         for k in range(self._isize[2]):
             for j in range(self._isize[1]):
                 for i in range(self._isize[0]):
                     yield primitives.iPoint(i, j, k)
コード例 #6
0
ファイル: microstructure.py プロジェクト: anilkunwar/OOF2
 def coords(self):
     if config.dimension() == 2:
         for j in range(self._isize[1]):
             for i in range(self._isize[0]):
                 yield primitives.iPoint(i, j)
     if config.dimension() == 3:
         for k in range(self._isize[2]):
             for j in range(self._isize[1]):
                 for i in range(self._isize[0]):
                     yield primitives.iPoint(i, j, k)
コード例 #7
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 def pixelFromPoint(self, where):
     xx = where.x / self._delta[0]
     if xx == 1.0 * self._isize[0]: xx = self._isize[0] - 1
     yy = where.y / self._delta[1]
     if yy == 1.0 * self._isize[1]: yy = self._isize[1] - 1
     if config.dimension() == 2:
         return primitives.iPoint(xx, yy)
     elif config.dimension() == 3:
         zz = where.z / self._delta[2]
         if zz == 1.0 * self._isize[2]: zz = self._isize[2] - 1
         return primitives.iPoint(xx, yy, zz)
コード例 #8
0
ファイル: microstructure.py プロジェクト: anilkunwar/OOF2
 def pixelFromPoint(self, where):
     xx=where.x/self._delta[0]
     if xx==1.0*self._isize[0]: xx=self._isize[0]-1
     yy=where.y/self._delta[1]
     if yy==1.0*self._isize[1]: yy=self._isize[1]-1
     if config.dimension() == 2:
         return primitives.iPoint(xx,yy)
     elif config.dimension() == 3:
         zz=where.z/self._delta[2]
         if zz==1.0*self._isize[2]: zz=self._isize[2]-1
         return primitives.iPoint(xx,yy,zz)
コード例 #9
0
ファイル: hkl.py プロジェクト: pk-organics/OOF3D
    def read(self, filename):
        hklfile = file(filename, "r")
        ## TODO  OPT: Use lineiter = iter(hklfile) instead of iter(lines).
        ## Then it's not necessary to create an array of lines.
        lines = hklfile.readlines()
        lineiter = iter(lines)
        line = lineiter.next()
        while not line.startswith('XCells'):
            line = lineiter.next()
        xcells = string.atoi(string.split(line)[1])
        line = lineiter.next()
        ycells = string.atoi(string.split(line)[1])
        line = lineiter.next()
        xstep = string.atof(string.split(line)[1])
        line = lineiter.next()
        ystep = string.atof(string.split(line)[1])
        line = lineiter.next()

        od = orientmapdata.OrientMap(
            primitives.iPoint(xcells, ycells),
            primitives.Point(xcells * xstep, ycells * ystep))

        while not string.split(line)[0] == 'Phase':
            line = lineiter.next()
        prog = progress.getProgress(os.path.basename(filename),
                                    progress.DEFINITE)
        try:
            count = 0
            npts = xcells * ycells
            for line in lineiter:
                vals = string.split(line)
                phase = vals[0]
                x = string.atof(vals[1])
                y = string.atof(vals[2])
                angles = map(string.atof, vals[5:8])
                mad = string.atof(vals[8])  # mean angular deviation
                ij = primitives.iPoint(int(round(x / xstep)),
                                       ycells - 1 - int(round(y / ystep)))
                try:
                    self.phaselists[phase].append(ij)
                except KeyError:
                    self.phaselists[phase] = [ij]
                self.set_angle(
                    od, ij,
                    corientation.COrientBunge(*map(math.radians, angles)))
                prog.setFraction(float(count) / npts)
                prog.setMessage("%d/%d orientations" % (count, npts))
                count += 1
                if pbar.stopped():
                    return None
        finally:
            prog.finish()
        return od
コード例 #10
0
ファイル: hkl.py プロジェクト: anilkunwar/OOF2
    def read(self, filename):
        hklfile = file(filename, "r")
        lineiter = iter(hklfile)
        line = lineiter.next()
        while not line.startswith('XCells'):
            line = lineiter.next()
        xcells = string.atoi(string.split(line)[1])
        line = lineiter.next()
        ycells = string.atoi(string.split(line)[1])
        line = lineiter.next()
        xstep = string.atof(string.split(line)[1])
        line = lineiter.next()
        ystep = string.atof(string.split(line)[1])
        line = lineiter.next()


        od = orientmapdata.OrientMap(
            primitives.iPoint(xcells, ycells),
            primitives.Point(xcells*xstep, ycells*ystep))
        
        while not string.split(line)[0] == 'Phase':
            line = lineiter.next()
        prog = progress.getProgress(os.path.basename(filename),
                                    progress.DEFINITE)
        try:
            count = 0
            npts = xcells*ycells
            for line in lineiter:
                vals = string.split(line)
                phase = vals[0]
                x = string.atof(vals[1])
                y = string.atof(vals[2])
                angles = map(string.atof, vals[5:8])
                mad = string.atof(vals[8])  # mean angular deviation
                ij = primitives.iPoint(
                    int(round(x/xstep)),
                    ycells-1-int(round(y/ystep)))
                try:
                    self.phaselists[phase].append(ij)
                except KeyError:
                    self.phaselists[phase] = [ij]
                self.set_angle(
                    od, ij, 
                    corientation.COrientBunge(*map(math.radians, angles)))
                prog.setFraction(float(count)/npts)
                prog.setMessage("%d/%d orientations" % (count, npts))
                count += 1
                if prog.stopped():
                    return None
        finally:
            prog.finish()
        return od
コード例 #11
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 def Load(self):
     from ooflib.common import primitives
     OOF.File.Load.Data(filename=reference_file("ms_data", "saved_ms"))
     ms_0 = getMicrostructure("save_test")
     self.assertEqual(ms_0.sizeInPixels(), primitives.iPoint(10, 10, 10))
     self.assertEqual(ms_0.size(), primitives.Point(2.5, 3.5, 4.5))
     self.assertEqual(ms_0.sizeOfPixels(), (2.5 / 10, 3.5 / 10, 4.5 / 10))
コード例 #12
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 def CreateMSFromImage(self):
     from ooflib.common import primitives
     OOF.Microstructure.Create_From_ImageFile(
         filenames=ThreeDImageDirectory(directory=reference_file(
             "ms_data", "jpeg"),
                                        sort=NumericalOrder()),
         microstructure_name=automatic,
         height=20.0,
         width=20.0,
         depth=20.0)
     OOF.Microstructure.Create_From_Image(name="new",
                                          width=automatic,
                                          height=automatic,
                                          image="jpeg:jpeg")
     ms_0 = getMicrostructure("jpeg")
     ms_1 = getMicrostructure("new")
     # Ensure images are separate objects.
     ms_1_image_id = id(ms_1.getImageContexts()[0])
     # Make sure the image wasn't copied in the source microstructure.
     self.assertEqual(len(ms_0.imageNames()), 1)
     # Make sure the newly constructed microstructure is the right size.
     self.assertEqual(ms_1.sizeInPixels(), primitives.iPoint(100, 100, 100))
     self.assertEqual(ms_1.size(), primitives.Point(20.0, 20.0, 20.0))
     self.assertEqual(ms_1.sizeOfPixels(),
                      (20.0 / 100, 20.0 / 100, 20.0 / 100))
     OOF.Microstructure.Delete(microstructure="jpeg")
     # Ensure that after the originating microstructure has been
     # deleted, the derived one still has the same image.
     self.assert_("jpeg" in ms_1.imageNames())
     self.assertEqual(ms_1_image_id, id(ms_1.getImageContexts()[0]))
コード例 #13
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 def Create_From_Image(self):
     from ooflib.common import primitives
     OOF.Microstructure.Create_From_ImageFile(filename=reference_file(
         "ms_data", "small.ppm"),
                                              microstructure_name=automatic,
                                              height=20.0,
                                              width=20.0)
     OOF.Microstructure.Create_From_Image(name="new",
                                          width=automatic,
                                          height=automatic,
                                          image="small.ppm:small.ppm")
     ms_0 = getMicrostructure("small.ppm")
     ms_1 = getMicrostructure("new")
     # Ensure images are separate objects.
     imageclass = whoville.getClass('Image')
     ms_1_image_id = id(ms_1.getImageContexts()[0])
     # Make sure the image wasn't copied in the source microstructure.
     self.assertEqual(len(ms_0.imageNames()), 1)
     # Make sure the newly constructed microstructure is the right size.
     self.assertEqual(ms_1.sizeInPixels(), primitives.iPoint(150, 150))
     self.assertEqual(ms_1.size(), primitives.Point(20.0, 20.0))
     self.assertEqual(ms_1.sizeOfPixels(), (20.0 / 150, 20.0 / 150))
     OOF.Microstructure.Delete(microstructure="small.ppm")
     # Ensure that after the originating microstructure has been
     # deleted, the derived one still has the same image.
     self.assert_("small.ppm" in ms_1.imageNames())
     self.assertEqual(ms_1_image_id, id(ms_1.getImageContexts()[0]))
コード例 #14
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 def Create_From_Image(self):
     from ooflib.common import primitives
     OOF.Microstructure.Create_From_ImageFile(
         filename=os.path.join("ms_data","jpeg","slice.jpg.*"),
         microstructure_name=automatic,
         height=20.0, width=20.0, depth=20.0)
     OOF.Microstructure.Create_From_Image(
         name="new", width=automatic, height=automatic,
         image="slice.jpg.*:slice.jpg.*")
     ms_0 = getMicrostructure("slice.jpg.*")
     ms_1 = getMicrostructure("new")
     # Ensure images are separate objects.
     ms_1_image_id = id(ms_1.getImageContexts()[0])
     # Make sure the image wasn't copied in the source microstructure.
     self.assertEqual(len(ms_0.imageNames()), 1)
     # Make sure the newly constructed microstructure is the right size.
     self.assertEqual(ms_1.sizeInPixels(), primitives.iPoint(100,100,100))
     self.assertEqual(ms_1.size(), primitives.Point(20.0, 20.0, 20.0))
     self.assertEqual(ms_1.sizeOfPixels(), (20.0/100, 20.0/100, 20.0/100))
     OOF.Microstructure.Delete(microstructure="slice.jpg.*")
     # Ensure that after the originating microstructure has been
     # deleted, the derived one still has the same image.
     self.assert_("slice.jpg.*" in ms_1.imageNames())
     self.assertEqual(ms_1_image_id, id(ms_1.getImageContexts()[0]))
     OOF.Microstructure.Delete(microstructure="new")
コード例 #15
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 def Create_From_ImageFile(self):
     from ooflib.SWIG.image import oofimage
     from ooflib.common import primitives
     from ooflib.SWIG.common.IO import stringimage
     self.assertRaises(
         oofimage.ImageMagickError, 
         OOF.Microstructure.Create_From_ImageFile,
         filename="nosuchfile", microstructure_name="nosuchfile",
         height=automatic, width=automatic)
     self.assertRaises(
         ooferror.ErrUserError,
         OOF.Microstructure.Create_From_ImageFile,
         filename=reference_file("ms_data","small.ppm"),
         microstructure_name="oops",
         height=-1.0, width=-1.0)
     OOF.Microstructure.Create_From_ImageFile(
         filename=reference_file("ms_data","small.ppm"),
         microstructure_name="small.ms",
         height=20.0, width=20.0)
     ms = getMicrostructure("small.ms")
     self.assertEqual(ms.size(), primitives.Point(20.0, 20.0))
     self.assertEqual(ms.sizeInPixels(), primitives.iPoint(150,150))
     self.assertEqual(ms.sizeOfPixels(), (20.0/150, 20.0/150))
     ms_images = ms.imageNames()
     self.assertEqual(len(ms_images), 1)
     self.assert_("small.ppm" in ms_images)
     img = oofimage.getImage("small.ms:small.ppm")
     strimg = stringimage.StringImage(ms.sizeInPixels(), ms.size())
     img.fillstringimage(strimg)
     outfile = file('hexstringimage.dat','w')
     print >> outfile, strimg.hexstringimage()
     outfile.close()
     assert filecmp.cmp('hexstringimage.dat',
                        reference_file('ms_data','smallppm.hex'))
     os.remove("hexstringimage.dat")
コード例 #16
0
 def properTile(self, point):
     ix = int(point.x * self.scale[0])
     iy = int(point.y * self.scale[1])
     # When right or top skeleton edge was clicked ....
     if ix == self.size[0]: ix -= 1
     if iy == self.size[1]: iy -= 1
     ##            if config.dimension() == 2:
     return primitives.iPoint(ix, iy)
コード例 #17
0
ファイル: skeletonnode.py プロジェクト: anilkunwar/OOF2
        def properTile(self, point):
            ix = int( point.x*self.scale[0] )
            iy = int( point.y*self.scale[1] )
            # When right or top skeleton edge was clicked ....
            if ix==self.size[0]: ix -= 1
            if iy==self.size[1]: iy -= 1
##            if config.dimension() == 2:
            return primitives.iPoint(ix, iy)
コード例 #18
0
ファイル: tsl.py プロジェクト: pk-organics/OOF3D
        def read(self, filepattern):
            dirname = os.path.dirname(filepattern)
            items = os.listdir(dirname)
            escaped_pattern = string.replace(
                re.escape(os.path.basename(filepattern)), "\\*", ".*?")
            files = []
            for item in items:
                match = re.match(escaped_pattern, item)
                if match != None:
                    span = match.span()
                    if span[0] == 0 and span[1] == len(item):
                        files.append(os.path.join(dirname, item))

            prog = progress.getProgress(os.path.basename(filepattern),
                                        progress.DEFINITE)

            try:
                # Look at the just the first file to get some info
                z = 0
                rows, npts = self.readfile(files[0], prog, z)
                nx = len(rows[0])
                ny = len(rows)
                nz = len(files)
                dx = rows[0][1].position[0] - rows[0][0].position[0]
                dy = rows[1][0].position[1] - rows[0][0].position[1]
                dz = 1
                pxlsize = primitives.Point(dx, dy, dz)
                size = rows[-1][-1].position + pxlsize
                od = orientmapdata.OrientMap(primitives.iPoint(nx, ny, nz),
                                             size)
                count = 0
                for row in rows:
                    count += 1
                    for datum in row:
                        self.addDatum(od, datum, pxlsize, ny, count, npts,
                                      prog, nz)

                # now look at the rest of the files
                for file in files[1:]:
                    z = z + dz
                    rows, nrowpts = self.readfile(file, prog, z)
                    npts = npts + nrowpts
                    count = 0
                    for row in rows:
                        count += 1
                        if len(row) != nx:
                            raise ooferror.ErrUserError(
                                "Orientation map data appears to be incomplete"
                            )

                        for datum in row:
                            self.addDatum(od, datum, pxlsize, ny, count, npts,
                                          prog, nz)

            finally:
                prog.finish()

            return od
コード例 #19
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 def Load(self):
     from ooflib.common import primitives
     # The MS in this file is named "load_test", and is the same
     # as the "save_test" one, except for the name.
     OOF.File.Load.Data(filename=reference_file("ms_data", "saved_ms"))
     ms_0 = getMicrostructure("save_test")
     self.assertEqual(ms_0.sizeInPixels(), primitives.iPoint(10, 10))
     self.assertEqual(ms_0.size(), primitives.Point(2.5, 3.5))
     self.assertEqual(ms_0.sizeOfPixels(), (2.5 / 10, 3.5 / 10))
コード例 #20
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 def Load(self):
     from ooflib.common import primitives
     # The MS in this file is named "load_test", and is the same
     # as the "save_test" one, except for the name.
     OOF.File.Load.Data(filename=reference_file("ms_data","saved_ms"))
     ms_0 = getMicrostructure("save_test")
     self.assertEqual(ms_0.sizeInPixels(), primitives.iPoint(10,10))
     self.assertEqual(ms_0.size(), primitives.Point(2.5, 3.5))
     self.assertEqual(ms_0.sizeOfPixels(), (2.5/10, 3.5/10 ))
コード例 #21
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 def Load(self):
     OOF.Microstructure.New(name="load_test",
                            width=100,
                            height=100,
                            depth=100,
                            width_in_pixels=100,
                            height_in_pixels=100,
                            depth_in_pixels=100)
     OOF.File.Load.Image(filenames=ThreeDImageDirectory(
         directory=reference_file("ms_data",
                                  "jpeg"), sort=NumericalOrder()),
                         microstructure="load_test",
                         height=automatic,
                         width=automatic,
                         depth=automatic)
     ms = getMicrostructure("load_test")
     ms_images = ms.imageNames()
     self.assertEqual(len(ms_images), 1)
     self.assert_("jpeg" in ms_images)
     # Check a few pixel values
     im = imagecontext.imageContexts['load_test:jpeg'].getObject()
     self.assertEqual(
         im[primitives.iPoint(0, 0, 0)],
         color.RGBColor(0.054901960784313725, 0.996078431372549,
                        0.9921568627450981))
     self.assertNotEqual(im[primitives.iPoint(0, 0, 0)],
                         color.RGBColor(0.054901960, 0.0, 0.99215686))
     # This voxel is selected in Direct_Pixel_Selection.Color in
     # pixel_test.py on Mac but not Linux.  Apparently Mac and
     # Linux use different jpeg libraries which decompress images
     # differently. WTF?
     ## TODO: Check that problem is avoided if vtk on Mac is
     ## compiled with USE_SYSTEM_JPEG=OFF
     self.assertEqual(
         im[primitives.iPoint(16, 9, 99)],
         # Linux value
         color.RGBColor(0.3058823529411765, 0.9921568627450981,
                        0.7215686274509804)
         # Mac value
         # color.RGBColor(
         #     0.2901960784313726,
         #     1.0,
         #     0.7372549019607844)
     )
コード例 #22
0
ファイル: tsl.py プロジェクト: pk-organics/OOF3D
        def read(self, filename):
            prog = progress.getProgress(os.path.basename(filename),
                                        progress.DEFINITE)
            rows, npts = self.readfile(filename, prog)

            try:

                nx = len(rows[0])
                ny = len(rows)
                count = 0
                for row in rows:
                    count += 1
                    if len(row) != nx:
                        raise ooferror.ErrUserError(
                            "Orientation map data appears to be incomplete")

                # pixel size
                dx = rows[0][1].position[0] - rows[0][0].position[0]
                dy = rows[1][0].position[1] - rows[0][0].position[1]
                pxlsize = primitives.Point(dx, dy)

                # If we assume that the points are in the centers of the
                # pixels, then the actual physical size is one pixel bigger
                # than the range of the xy values.
                size = rows[-1][-1].position + pxlsize

                debug.fmsg("nx=", nx, "ny=", ny, "size=", size, "pxlsize=",
                           pxlsize)

                if config.dimension() == 2:
                    od = orientmapdata.OrientMap(primitives.iPoint(nx, ny),
                                                 size)
                else:
                    od = orientmapdata.OrientMap(primitives.iPoint(nx, ny, 1),
                                                 size)
                count = 0
                for row in rows:
                    for datum in row:
                        self.addDatum(od, datum, pxlsize, ny, count, npts,
                                      prog)

            finally:
                prog.finish()
            return od
コード例 #23
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 def draw_image(self, image, offset, size):
     if image.sizeInPixels() == iPoint(0, 0):
         return
     pdfid = len(self.objects)
     self.objects.append(0)  # Place-holder.
     newimage = PDFImageObject(pdfid, image, offset, size)
     self.images.append(newimage)
     self.current_layer.add_image(newimage)
     self.expand_range(
         Rectangle(offset, Coord(offset[0] + size[0], offset[1] + size[1])))
コード例 #24
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ファイル: skeletonnode.py プロジェクト: anilkunwar/OOF2
 def nextBand(self, ll=None, ur=None):
     nodes = []
     # Bottom
     j = ll.y
     for i in range(ll.x, ur.x+1):
         nodes += self[primitives.iPoint(i,j)][:]
     # Top
     j = ur.y
     for i in range(ll.x, ur.x+1):
         nodes += self[primitives.iPoint(i,j)][:]
     # Left
     i = ll.x
     for j in range(ll.y+1, ur.y):
         nodes += self[primitives.iPoint(i,j)][:]
     # Right
     i = ur.x
     for j in range(ll.y+1, ur.y):
         nodes += self[primitives.iPoint(i,j)][:]
     return nodes
コード例 #25
0
ファイル: pdfoutput.py プロジェクト: anilkunwar/OOF2
    def draw_image(self,image,offset,size):
	if image.sizeInPixels()==iPoint(0,0):
            return
        pdfid = len(self.objects)
        self.objects.append(0) # Place-holder.
        newimage = PDFImageObject(pdfid,image,offset,size)
        self.images.append(newimage)
        self.current_layer.add_image(newimage)
        self.expand_range(Rectangle(offset,Coord(offset[0]+size[0],
                                                 offset[1]+size[1])))
コード例 #26
0
def newMicrostructure_Parallel(menuitem, name, width, height, width_in_pixels,
                               height_in_pixels):
    # Only for the back-end processes
    global _rank
    if _rank == 0:
        return

    ms = ooflib.common.microstructure.Microstructure(
        name, primitives.iPoint(width_in_pixels, height_in_pixels),
        primitives.Point(width, height))
コード例 #27
0
 def nextBand(self, ll=None, ur=None):
     nodes = []
     # Bottom
     j = ll.y
     for i in range(ll.x, ur.x + 1):
         nodes += self[primitives.iPoint(i, j)][:]
     # Top
     j = ur.y
     for i in range(ll.x, ur.x + 1):
         nodes += self[primitives.iPoint(i, j)][:]
     # Left
     i = ll.x
     for j in range(ll.y + 1, ur.y):
         nodes += self[primitives.iPoint(i, j)][:]
     # Right
     i = ur.x
     for j in range(ll.y + 1, ur.y):
         nodes += self[primitives.iPoint(i, j)][:]
     return nodes
コード例 #28
0
ファイル: microstructureIO.py プロジェクト: creuzige/OOF2
    def __init__(self, array):
        # array is a list of lists of Ints, which are pixel categories
        self.pxls = {}  # list of pixels, keyed by category
        for j, sublist in enumerate(array):
            if config.dimension() == 2:
                for i, category in enumerate(sublist):
                    where = primitives.iPoint(i, j)
                    try:
                        self.pxls[category].append(where)
                    except KeyError:
                        self.pxls[category] = [where]

            elif config.dimension() == 3:
                for i, subsublist in enumerate(sublist):
                    for k, category in enumerate(subsublist):
                        where = primitives.iPoint(k, i, j)
                        try:
                            self.pxls[category].append(where)
                        except KeyError:
                            self.pxls[category] = [where]
コード例 #29
0
ファイル: microstructureIO.py プロジェクト: shkeshavarz/OOF2
    def __init__(self, array):
        # array is a list of lists of Ints, which are pixel categories
        self.pxls = {}  # list of pixels, keyed by category
        for j, sublist in enumerate(array):
            if config.dimension() == 2:
                for i, category in enumerate(sublist):
                    where = primitives.iPoint(i, j)
                    try:
                        self.pxls[category].append(where)
                    except KeyError:
                        self.pxls[category] = [where]

            elif config.dimension() == 3:
                for i, subsublist in enumerate(sublist):
                    for k, category in enumerate(subsublist):
                        where = primitives.iPoint(k, i, j)
                        try:
                            self.pxls[category].append(where)
                        except KeyError:
                            self.pxls[category] = [where]
コード例 #30
0
 def draw_shaped_image(self, image, offset, size, shapecolor):
     ## No longer used in OOF
     if image.sizeInPixels() == iPoint(0, 0):
         return
     pdfid = len(self.objects)
     self.objects.append(0)  # Place-holder
     newimage = PDFShapedImageObject(pdfid, image, offset, size, shapecolor)
     self.images.append(newimage)
     self.current_layer.add_image(newimage)
     self.expand_range(
         Rectangle(offset, Coord(offset[0] + size[0], offset[1] + size[1])))
コード例 #31
0
ファイル: pdfoutput.py プロジェクト: anilkunwar/OOF2
 def draw_shaped_image(self,image,offset,size,shapecolor):
     ## No longer used in OOF
     if image.sizeInPixels()==iPoint(0,0):
         return
     pdfid = len(self.objects)
     self.objects.append(0) # Place-holder
     newimage = PDFShapedImageObject(pdfid,image,offset,size,shapecolor)
     self.images.append(newimage)
     self.current_layer.add_image(newimage)
     self.expand_range(Rectangle(offset,Coord(offset[0]+size[0],
                                              offset[1]+size[1])) )
コード例 #32
0
ファイル: pdfoutput.py プロジェクト: anilkunwar/OOF2
 def draw_alpha_image(self, bitmap, offset, size):
     if bitmap.sizeInPixels()==iPoint(0,0):
         return
     pdfid = len(self.objects)
     self.objects.append(0) # Place-holder
     maskcolor = bitmap.getBG()
     newimage = PDFShapedImageObject(pdfid,bitmap,offset,size,maskcolor)
     self.images.append(newimage)
     self.current_layer.add_image(newimage)
     self.current_layer.set_alpha(bitmap.getTintAlpha())
     self.expand_range(Rectangle(offset,Coord(offset[0]+size[0],
                                              offset[1]+size[1])) )
コード例 #33
0
 def draw_alpha_image(self, bitmap, offset, size):
     if bitmap.sizeInPixels() == iPoint(0, 0):
         return
     pdfid = len(self.objects)
     self.objects.append(0)  # Place-holder
     maskcolor = bitmap.getBG()
     newimage = PDFShapedImageObject(pdfid, bitmap, offset, size, maskcolor)
     self.images.append(newimage)
     self.current_layer.add_image(newimage)
     self.current_layer.set_alpha(bitmap.getTintAlpha())
     self.expand_range(
         Rectangle(offset, Coord(offset[0] + size[0], offset[1] + size[1])))
コード例 #34
0
ファイル: tsl.py プロジェクト: santiama/OOF3D
 def addDatum(self, od, datum, pxlsize, ny, count, npts, prog, nz=0):
     prog.setMessage("Processing orientations %d/%d" % (count,npts))
     if config.dimension() == 2:
         ij = primitives.iPoint(
             int(round(datum.position[0]/pxlsize[0])),
             ny-1-int(round(datum.position[1]/pxlsize[1])))
     elif config.dimension() == 3:
         ij = primitives.iPoint(
             int(round(datum.position[0]/pxlsize[0])),
             ny-1-int(round(datum.position[1]/pxlsize[1])),
             nz-1-int(round(datum.position[2]/pxlsize[2])))
     try:
         self.phaselists[datum.phasename].append(ij)
     except KeyError:
         self.phaselists[datum.phasename] = [ij]
     self.set_angle(od, ij, datum.euler())
     prog.setMessage("%d/%d orientations" % (count,npts))
     prog.setFraction(float(count)/npts)
     count += 1
     if prog.stopped():
         return None
コード例 #35
0
ファイル: voxelinfoGUI.py プロジェクト: santiama/OOF3D
 def updateButtonCB(self, button):
     debug.mainthreadTest()
     self.updatebutton.set_sensitive(0)
     x = int(self.xtext.get_text())
     y = int(self.ytext.get_text())
     z = int(self.ztext.get_text())
     msOrImage = self.gfxwindow().topmost('Microstructure', 'Image')
     size = msOrImage.sizeInPixels()
     if x < 0 or x >= size.x or y < 0 or y >= size.y \
            or z < 0 or z >= size.z: # illegal point
         self.update()  # restore original values
         return
     self.toolbox.menu.QueryDirectly(voxel=primitives.iPoint(x, y, z))
コード例 #36
0
ファイル: microstructureIPC.py プロジェクト: anilkunwar/OOF2
def newMicrostructure_Parallel(menuitem, name,
                               width, height,
                               width_in_pixels, height_in_pixels):
    # Only for the back-end processes
    global _rank
    if _rank == 0:
        return
    
    ms = ooflib.common.microstructure.Microstructure(
        name, primitives.iPoint(width_in_pixels,
                                height_in_pixels),
        primitives.Point(width, height)
        )
コード例 #37
0
ファイル: microstructuremenu.py プロジェクト: anilkunwar/OOF2
    def newMicrostructure(menuitem, name,
                          width, height,
                          width_in_pixels, height_in_pixels):
        if width<=0 or height<=0 or width_in_pixels<=0 or height_in_pixels<=0:
            raise ooferror.ErrUserError("Negative size values are not allowed.")

        if parallel_enable.enabled():
            # For the rear-end guys
            microstructureIPC.msmenu.New_Parallel(name=name,
                                                 width=width, height=height,
                                                 width_in_pixels=width_in_pixels,
                                                 height_in_pixels=height_in_pixels)

        # Serial mode & #0 in parallel mode
        ms = ooflib.common.microstructure.Microstructure(
            name, primitives.iPoint(width_in_pixels,
                                    height_in_pixels),
            primitives.Point(width, height)
            )
コード例 #38
0
ファイル: microstructuremenu.py プロジェクト: song2001/OOF2
    def newMicrostructure(menuitem, name, width, height, width_in_pixels,
                          height_in_pixels):
        if width <= 0 or height <= 0 or width_in_pixels <= 0 or height_in_pixels <= 0:
            raise ooferror.ErrUserError(
                "Negative size values are not allowed.")

        if parallel_enable.enabled():
            # For the rear-end guys
            microstructureIPC.msmenu.New_Parallel(
                name=name,
                width=width,
                height=height,
                width_in_pixels=width_in_pixels,
                height_in_pixels=height_in_pixels)

        # Serial mode & #0 in parallel mode
        ms = ooflib.common.microstructure.Microstructure(
            name, primitives.iPoint(width_in_pixels, height_in_pixels),
            primitives.Point(width, height))
コード例 #39
0
ファイル: microstructure_test.py プロジェクト: song2001/OOF2
 def Create_From_ImageFile(self):
     from ooflib.image import oofimage3d
     from ooflib.common import primitives
     from ooflib.SWIG.common.IO import stringimage
     self.assertRaises(ooferror.ErrUserError,
                       OOF.Microstructure.Create_From_ImageFile,
                       filename="nosuchfile",
                       microstructure_name="nosuchfile",
                       height=automatic,
                       width=automatic,
                       depth=automatic)
     self.assertRaises(ooferror.ErrUserError,
                       OOF.Microstructure.Create_From_ImageFile,
                       filename=os.path.join("ms_data", "jpeg",
                                             "slice.jpg.*"),
                       microstructure_name="oops",
                       height=-1.0,
                       width=-1.0,
                       depth=-1.0)
     OOF.Microstructure.Create_From_ImageFile(
         filename=os.path.join("ms_data", "jpeg", "slice.jpg.*"),
         microstructure_name="slice.jpg.*",
         height=20.0,
         width=20.0,
         depth=20.0)
     ms = getMicrostructure("slice.jpg.*")
     self.assertEqual(ms.size(), primitives.Point(20.0, 20.0, 20.0))
     self.assertEqual(ms.sizeInPixels(), primitives.iPoint(100, 100, 100))
     self.assertEqual(ms.sizeOfPixels(),
                      (20.0 / 100, 20.0 / 100, 20.0 / 100))
     ms_images = ms.imageNames()
     self.assertEqual(len(ms_images), 1)
     self.assert_("slice.jpg.*" in ms_images)
     img = oofimage3d.getImage("slice.jpg.*:slice.jpg.*")
     ##        strimg = stringimage.StringImage(ms.sizeInPixels(), ms.size())
     ##         img.fillstringimage(strimg)
     ##         outfile = file('hexstringimage.dat','w')
     ##         print >> outfile, strimg.hexstringimage()
     ##         outfile.close()
     ##         assert filecmp.cmp('hexstringimage.dat',
     ##                            os.path.join('ms_data','smallppm.hex'))
     ##         os.remove("hexstringimage.dat")
     OOF.Microstructure.Delete(microstructure="slice.jpg.*")
コード例 #40
0
ファイル: voxelinfoGUI.py プロジェクト: santiama/OOF3D
 def up(self, x, y, shift, ctrl):
     msOrImage = self.gfxwindow().topmost('Microstructure', 'Image')
     if msOrImage:
         if config.dimension() == 3:
             canvas = self.toolbox.gfxwindow().oofcanvas
             view = canvas.get_view()
             pt = canvas.display2Physical(view, x, y)
             if pt is not None:
                 self.toolbox.menu.Query(point=pt, view=view)
         else:
             pt = primitives.iPoint(x, y)
             self.toolbox.menu.Query(point=pt)
         # p = self.gfxwindow().oofcanvas.screen_coords_to_3D_coords(x,y)
         # if p is not None:
         #     where = msOrImage.pixelFromPoint(
         #         primitives.Point(p[0],p[1],p[2]));
         #     if where is not None:
         #         self.toolbox.menu.Query(x=where[0], y=where[1], z=where[2])
     else:
         for plugin in self.plugins:
             plugin.nonsense()
コード例 #41
0
 def Create_From_ImageFile(self):
     from ooflib.SWIG.image import oofimage
     from ooflib.common import primitives
     from ooflib.SWIG.common.IO import stringimage
     self.assertRaises(oofimage.ImageMagickError,
                       OOF.Microstructure.Create_From_ImageFile,
                       filename="nosuchfile",
                       microstructure_name="nosuchfile",
                       height=automatic,
                       width=automatic)
     self.assertRaises(ooferror.ErrUserError,
                       OOF.Microstructure.Create_From_ImageFile,
                       filename=reference_file("ms_data", "small.ppm"),
                       microstructure_name="oops",
                       height=-1.0,
                       width=-1.0)
     OOF.Microstructure.Create_From_ImageFile(
         filename=reference_file("ms_data", "small.ppm"),
         microstructure_name="small.ms",
         height=20.0,
         width=20.0)
     ms = getMicrostructure("small.ms")
     self.assertEqual(ms.size(), primitives.Point(20.0, 20.0))
     self.assertEqual(ms.sizeInPixels(), primitives.iPoint(150, 150))
     self.assertEqual(ms.sizeOfPixels(), (20.0 / 150, 20.0 / 150))
     ms_images = ms.imageNames()
     self.assertEqual(len(ms_images), 1)
     self.assert_("small.ppm" in ms_images)
     img = oofimage.getImage("small.ms:small.ppm")
     strimg = stringimage.StringImage(ms.sizeInPixels(), ms.size())
     img.fillstringimage(strimg)
     outfile = file('hexstringimage.dat', 'w')
     print >> outfile, strimg.hexstringimage()
     outfile.close()
     assert filecmp.cmp('hexstringimage.dat',
                        reference_file('ms_data', 'smallppm.hex'))
     os.remove("hexstringimage.dat")
コード例 #42
0
    def Create_From_ImageFile(self):
        from ooflib.image import oofimage3d
        from ooflib.common import primitives
        from ooflib.SWIG.common.IO import stringimage
        self.assertRaises(
            ooferror.ErrUserError, 
            OOF.Microstructure.Create_From_ImageFile,
            filename="nosuchfile", microstructure_name="nosuchfile",
            height=automatic, width=automatic, depth=automatic)
        self.assertRaises(
            ooferror.ErrUserError,
            OOF.Microstructure.Create_From_ImageFile,
            filename=os.path.join("ms_data","jpeg","slice.jpg.*"),
            microstructure_name="oops",
            height=-1.0, width=-1.0, depth=-1.0)
        OOF.Microstructure.Create_From_ImageFile(
            filename=os.path.join("ms_data","jpeg","slice.jpg.*"),
            microstructure_name="slice.jpg.*",
            height=20.0, width=20.0, depth=20.0)
        ms = getMicrostructure("slice.jpg.*")
        self.assertEqual(ms.size(), primitives.Point(20.0, 20.0, 20.0))
        self.assertEqual(ms.sizeInPixels(), primitives.iPoint(100,100,100))
        self.assertEqual(ms.sizeOfPixels(), (20.0/100, 20.0/100, 20.0/100))
        ms_images = ms.imageNames()
        self.assertEqual(len(ms_images), 1)
        self.assert_("slice.jpg.*" in ms_images)
        img = oofimage3d.getImage("slice.jpg.*:slice.jpg.*")
##        strimg = stringimage.StringImage(ms.sizeInPixels(), ms.size())
##         img.fillstringimage(strimg)
##         outfile = file('hexstringimage.dat','w')
##         print >> outfile, strimg.hexstringimage()
##         outfile.close()
##         assert filecmp.cmp('hexstringimage.dat',
##                            os.path.join('ms_data','smallppm.hex'))
##         os.remove("hexstringimage.dat")
        OOF.Microstructure.Delete(microstructure="slice.jpg.*")
コード例 #43
0
ファイル: oofimage3d.py プロジェクト: anilkunwar/OOF2
 def setup(self):
     sighs = self.image.GetDimensions()
     # subtract 1 because of padding
     self._sizeInPixels = primitives.iPoint(sighs[0]-1, sighs[1]-1, sighs[2]-1)
コード例 #44
0
ファイル: tsl.py プロジェクト: anilkunwar/OOF2
    def _read(self, tslfile, prog):
        data, hexgrid = self.readData(tslfile, prog)
        npts = len(data)
        rows = list(getrows(data)) # sorts data
        if hexgrid is None:
            # readData didn't set hexgrid.  The grid is hexagonal if
            # the first two rows don't start at the same x.
            hexgrid = rows[0][0].position[0] != rows[1][0].position[0]

        if hexgrid:
            # Throw out every other row.
            reporter.warn(
                "Converting hexagonal lattice to rectangular"
                " by discarding alternate rows.")
            rows = rows[::2]            # discard odd numbered rows

        nx = len(rows[0])
        ny = len(rows)
        count = 0
        for row in rows:
            count += 1
            if len(row) != nx:
                raise ooferror.ErrUserError(
                    "Orientation map data appears to be incomplete.\n"
                    "len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))

        # TSL puts the origin at the top left, so it's using a left
        # handed coordinate system!  If flip_y==True, fix that.  Also,
        # make sure there are no negative x or y values.
        ymax = rows[-1][0].position[1]
        ymin = rows[0][0].position[1]
        xmax = rows[0][-1].position[0]
        xmin = rows[0][0].position[0]
        for row in rows:
            for point in row:
                if self.flip_x:
                    point.position[0] = xmax - point.position[0]
                else:
                    point.position[0] = point.position[0] - xmin
                if self.flip_y:
                    point.position[1] = ymax - point.position[1]
                else:
                    point.position[1] = point.position[1] - ymin
    
        # If flipped, the rows are still ordered top to bottom, but
        # the coordinates increase bottom to top.

        # pixel size
        dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
        dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
        pxlsize = primitives.Point(dx, dy)
        
        width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
        height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
        # If we assume that the points are in the centers of the
        # pixels, then the actual physical size is one pixel bigger
        # than the range of the xy values.
        size = primitives.Point(width, height) + pxlsize

        od = orientmapdata.OrientMap(primitives.iPoint(nx, ny), size)
        prog.setMessage("%d/%d orientations" % (0, npts))
        count = 0
        for row in rows:
            for datum in row:
                ij = primitives.iPoint(
                    int(round(datum.position[0]/pxlsize[0])),
                    int(round(datum.position[1]/pxlsize[1])))
                try:
                    self.phaselists[datum.phasename].append(ij)
                except KeyError:
                    self.phaselists[datum.phasename] = [ij]
                self.set_angle(od, ij, datum.euler())
                prog.setMessage("%d/%d orientations" % (count,npts))
                prog.setFraction(float(count)/npts)
                count += 1
                if prog.stopped():

                    return None
        prog.finish()
        return od
コード例 #45
0
ファイル: pointparameter.py プロジェクト: pk-organics/OOF3D
 def binaryRead(self, parser):
     b = parser.getBytes(iPointParameter.structlen)
     vals = struct.unpack(iPointParameter.structfmt, b)
     return primitives.iPoint(*vals)
コード例 #46
0
def writeMicrostructure(datafile, mscontext):
    ms = mscontext.getObject()

    mscontext.begin_reading()
    try:
        datafile.startCmd(OOF.LoadData.Microstructure.New)
        datafile.argument('name', ms.name())
        datafile.argument('size', ms.size())
        datafile.argument('isize', ms.sizeInPixels())
        datafile.endCmd()

        for ioplugin in _ioplugins:
            ioplugin(datafile, mscontext)
##        for image in ms.getImageContexts():
##            image.writeImage(datafile)

# Store pixel attributes by storing category definitions.
        for grpname in ms.groupNames():
            grp = ms.findGroup(grpname)
            datafile.startCmd(OOF.LoadData.Microstructure.PixelGroup)
            datafile.argument('microstructure', ms.name())
            datafile.argument('group', grpname)
            datafile.argument('meshable', grp.is_meshable())
            datafile.endCmd()
        # Create the actual active areas themselves.
        for aaname in ms.activeAreaNames():
            datafile.startCmd(OOF.LoadData.Microstructure.NewActiveArea)
            datafile.argument('microstructure', ms.name())
            datafile.argument('name', aaname)
            datafile.endCmd()
        categories = ms.getCategoryMapRO()
        # Save categories
        datafile.startCmd(OOF.LoadData.Microstructure.Categories)
        datafile.argument('microstructure', ms.name())
        datafile.argument('categories', categories)
        datafile.endCmd()
        # Find representative pixels for each category TODO 3.1: The
        # underlying code no longer uses representative pixels. There
        # may be a more efficient way to do this using
        # attributeVectorSet. Do this when moving to C.
        reppxls = {}
        i = 0
        if config.dimension() == 2:
            for row in categories:
                j = 0
                for ctgry in row:
                    reppxls[ctgry] = primitives.iPoint(j, i)
                    j += 1
                i += 1
        elif config.dimension() == 3:
            for slab in categories:
                j = 0
                for row in slab:
                    k = 0
                    for ctgry in row:
                        reppxls[ctgry] = primitives.iPoint(j, i, k)
                        k += 1
                    j += 1
                i += 1
        # Save definitions of pixel categories
        for i in range(pixelattribute.nAttributes()):
            reg = pixelattribute.getRegistration(i)
            # debug.fmsg("Writing category data for", reg.name())
            reg.writeGlobalData(datafile, ms)
            for category in range(len(reppxls)):
                reppxl = reppxls[category]
                datafile.startCmd(
                    getattr(OOF.LoadData.Microstructure.DefineCategory,
                            reg.name()))
                datafile.argument('microstructure', ms.name())
                datafile.argument('category', category)
                if reg.writeData(datafile, ms, reppxl):
                    datafile.endCmd()
                    # debug.fmsg("wrote data for category", category)
                else:
                    datafile.discardCmd()
                    # debug.fmsg("oops, nothing written for category", category)
        datafile.startCmd(OOF.LoadData.Microstructure.EndCategories)
        datafile.argument('microstructure', ms.name())
        datafile.endCmd()

        #Interface branch
        #Note that materials that are not assigned to pixels do not get saved
        #when the microstructure is saved, if we rely on the above mechanism
        #(reg.writeGlobalData is not called for these materials).
        for ioplugin in _ioplugins_last:
            ioplugin(datafile, mscontext)

    finally:
        mscontext.end_reading()
コード例 #47
0
imageGeoFilter = vtk.vtkImageDataGeometryFilter()
imageGeoFilter.SetInput(indexedImage)
imageGeoFilter.SetExtent(imageBounds)
imagePoints = imageGeoFilter.GetOutput()
imagePoints.Update()

# needed to calulate normal and area
polygon = vtk.vtkPolygon()
triangle = vtk.vtkTriangle()
normal = [0.0,0.0,0.0]
pt=[0.0,0.0,0.0]
# loop over voxels and add faces that border different pixel groups to polydata
for i in xrange(indexedImage.GetNumberOfCells()):
    voxel = indexedImage.GetCell(i)
    p = voxel.GetPoints().GetPoint(0)
    point = primitives.iPoint(p[0]-x0,p[1]-y0,p[2]-z0)
    value = indexedImage.GetScalarComponentAsFloat(point[0],point[1],point[2],0)
    for j in xrange(6):
        point2 = point+dirs[j]
        if point2[0] >= imageBounds[0] and point2[0] <= imageBounds[1]-1 and point2[1] >= imageBounds[2] and point2[1] <= imageBounds[3]-1 and point2[2] >= imageBounds[4] and point2[2] <= imageBounds[5]-1:
            value2 = indexedImage.GetScalarComponentAsFloat(point2[0],point2[1],point2[2],0)
            if value2 != value:
                # only add face for the given value, so that we don't
                # get double faces and so that the normal points
                # outward.
                face=voxel.GetFace(j)
                quadpoints = vtk.vtkPoints()
                # We have to explicity make the quad because, very annoyingly,
                # the order of points in the voxels and pixels returned by
                # vtkImageData are not compatible with the quads used for
                # polydata.
コード例 #48
0
ファイル: genericreader.py プロジェクト: anilkunwar/OOF2
    def _read(self, datafile, prog):
        # readData gets data from the file, but does no processing
        data = self.readData(datafile, prog)
        rows = list(getrows(data)) # sorts data
        # The grid is hexagonal if the first two rows don't start at the same x.
        if rows[0][0].position[0] != rows[1][0].position[0]:
            # Throw out every other row.
            reporter.warn(
                "Converting hexagonal lattice to rectangular"
                " by discarding alternate rows.")
            rows = rows[::2]    # discard odd numbered rows

        # Check that all rows are the same length, and flip the
        # coordinates if requested.
        nx = len(rows[0])
        ny = len(rows)
        ymax = rows[-1][0].position[1]
        ymin = rows[0][0].position[1]
        xmax = rows[0][-1].position[0]
        xmin = rows[0][0].position[0]
        count = 0
        for row in rows:
            count += 1
            if len(row) != nx:
                raise ooferror.ErrUserError(
                    "Orientation map data appears to be incomplete.\n"
                    "len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))
            for point in row:
                if self.flip_x:
                    point.position[0] = xmax - point.position[0]
                else:
                    point.position[0] = point.position[0] - xmin
                if self.flip_y:
                    point.position[1] = ymax - point.position[1]
                else:
                    point.position[1] = point.position[1] - ymin

        # pixel size
        dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
        dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
        pxlsize = primitives.Point(dx, dy)

        width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
        height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
        # If we assume that the points are in the centers of the
        # pixels, then the actual physical size is one pixel bigger
        # than the range of the xy values.
        size = primitives.Point(width, height) + pxlsize

        npts = len(rows)*len(rows[0])

        od = orientmapdata.OrientMap(primitives.iPoint(nx, ny),
                                     size*self.scale_factor)
        prog.setMessage("%d/%d orientations" % (0, npts))
        count = 0
        for row in rows:
            for datum in row:
                ij = primitives.iPoint(
                    int(round(datum.position[0]/pxlsize[0])),
                    int(round(datum.position[1]/pxlsize[1])))
                for groupname in datum.groups:
                    try:
                        self.groupmembers[groupname].append(ij)
                    except KeyError:
                        self.groupmembers[groupname] = [ij]
                if self.angle_units == 'Degrees':
                    offset = math.radians(self.angle_offset)
                    angleargs = datum.angletuple
                else:           # angle units are Radians
                    offset = self.angle_offset
                    # All Orientation subclasses that take angle args
                    # assume that they're in degrees.  They have a
                    # static radians2Degrees method that converts the
                    # angle args from radians to degrees.
                    angleargs = self.angle_type.radians2Degrees(
                        *datum.angletuple)
                # Create an instance of the Orientation subclass.
                orient = self.angle_type(*angleargs)
                if self.angle_offset != 0:
                    orient = orient.rotateXY(self.angle_offset)

                # Insert this point into the OrientMap object.
                self.set_angle(od, ij, orient.corient)

                prog.setMessage("%d/%d orientations" % (count, npts))
                prog.setFraction(float(count)/npts)
                count += 1
                if prog.stopped():
                    return None
        return od
コード例 #49
0
ファイル: microstructureIO.py プロジェクト: shkeshavarz/OOF2
def writeMicrostructure(datafile, mscontext):
    ms = mscontext.getObject()

    mscontext.begin_reading()
    try:
        datafile.startCmd(OOF.LoadData.Microstructure.New)
        datafile.argument("name", ms.name())
        datafile.argument("size", ms.size())
        datafile.argument("isize", ms.sizeInPixels())
        datafile.endCmd()

        for ioplugin in _ioplugins:
            ioplugin(datafile, mscontext)
        ##        for image in ms.getImageContexts():
        ##            image.writeImage(datafile)

        # Store pixel attributes by storing category definitions.
        for grpname in ms.groupNames():
            grp = ms.findGroup(grpname)
            datafile.startCmd(OOF.LoadData.Microstructure.PixelGroup)
            datafile.argument("microstructure", ms.name())
            datafile.argument("group", grpname)
            datafile.argument("meshable", grp.is_meshable())
            datafile.endCmd()
        # Create the actual active areas themselves.
        for aaname in ms.activeAreaNames():
            datafile.startCmd(OOF.LoadData.Microstructure.NewActiveArea)
            datafile.argument("microstructure", ms.name())
            datafile.argument("name", aaname)
            datafile.endCmd()
        categories = ms.getCategoryMapRO()
        # Save categories
        datafile.startCmd(OOF.LoadData.Microstructure.Categories)
        datafile.argument("microstructure", ms.name())
        datafile.argument("categories", categories)
        datafile.endCmd()
        # Find representative pixels for each category
        reppxls = {}
        i = 0
        if config.dimension() == 2:
            for row in categories:
                j = 0
                for ctgry in row:
                    reppxls[ctgry] = primitives.iPoint(j, i)
                    j += 1
                i += 1
        elif config.dimension() == 3:
            for slab in categories:
                j = 0
                for row in slab:
                    k = 0
                    for ctgry in row:
                        reppxls[ctgry] = primitives.iPoint(k, j, i)
                        k += 1
                    j += 1
                i += 1
        # Save definitions of pixel categories
        for i in range(pixelattribute.nAttributes()):
            reg = pixelattribute.getRegistration(i)
            reg.writeGlobalData(datafile, ms)
            for category in range(len(reppxls)):
                reppxl = reppxls[category]
                datafile.startCmd(getattr(OOF.LoadData.Microstructure.DefineCategory, reg.name()))
                datafile.argument("microstructure", ms.name())
                datafile.argument("category", category)
                if reg.writeData(datafile, ms, reppxl):
                    datafile.endCmd()
                else:
                    datafile.discardCmd()
        datafile.startCmd(OOF.LoadData.Microstructure.EndCategories)
        datafile.argument("microstructure", ms.name())
        datafile.endCmd()

        # Interface branch
        # Note that materials that are not assigned to pixels do not get saved
        # when the microstructure is saved, if we rely on the above mechanism
        # (reg.writeGlobalData is not called for these materials).
        for ioplugin in _ioplugins_last:
            ioplugin(datafile, mscontext)

    finally:
        mscontext.end_reading()
コード例 #50
0
    def _read(self, datafile, prog):
        # readData gets data from the file, but does no processing
        data = self.readData(datafile, prog)
        rows = list(getrows(data))  # sorts data
        # The grid is hexagonal if the first two rows don't start at the same x.
        if rows[0][0].position[0] != rows[1][0].position[0]:
            # Throw out every other row.
            reporter.warn("Converting hexagonal lattice to rectangular"
                          " by discarding alternate rows.")
            rows = rows[::2]  # discard odd numbered rows

        # Check that all rows are the same length, and flip the
        # coordinates if requested.
        nx = len(rows[0])
        ny = len(rows)
        ymax = rows[-1][0].position[1]
        ymin = rows[0][0].position[1]
        xmax = rows[0][-1].position[0]
        xmin = rows[0][0].position[0]
        count = 0
        for row in rows:
            count += 1
            if len(row) != nx:
                raise ooferror.ErrUserError(
                    "Orientation map data appears to be incomplete.\n"
                    "len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))
            for point in row:
                if self.flip_x:
                    point.position[0] = xmax - point.position[0]
                else:
                    point.position[0] = point.position[0] - xmin
                if self.flip_y:
                    point.position[1] = ymax - point.position[1]
                else:
                    point.position[1] = point.position[1] - ymin

        # pixel size
        dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
        dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
        pxlsize = primitives.Point(dx, dy)

        width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
        height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
        # If we assume that the points are in the centers of the
        # pixels, then the actual physical size is one pixel bigger
        # than the range of the xy values.
        size = primitives.Point(width, height) + pxlsize

        npts = len(rows) * len(rows[0])

        od = orientmapdata.OrientMap(primitives.iPoint(nx, ny),
                                     size * self.scale_factor)
        prog.setMessage("%d/%d orientations" % (0, npts))
        count = 0
        for row in rows:
            for datum in row:
                ij = primitives.iPoint(
                    int(round(datum.position[0] / pxlsize[0])),
                    int(round(datum.position[1] / pxlsize[1])))
                for groupname in datum.groups:
                    try:
                        self.groupmembers[groupname].append(ij)
                    except KeyError:
                        self.groupmembers[groupname] = [ij]
                if self.angle_units == 'Degrees':
                    offset = math.radians(self.angle_offset)
                    angleargs = datum.angletuple
                else:  # angle units are Radians
                    offset = self.angle_offset
                    # All Orientation subclasses that take angle args
                    # assume that they're in degrees.  They have a
                    # static radians2Degrees method that converts the
                    # angle args from radians to degrees.
                    angleargs = self.angle_type.radians2Degrees(
                        *datum.angletuple)
                # Create an instance of the Orientation subclass.
                orient = self.angle_type(*angleargs)
                if self.angle_offset != 0:
                    orient = orient.rotateXY(self.angle_offset)

                # Insert this point into the OrientMap object.
                self.set_angle(od, ij, orient.corient)

                prog.setMessage("%d/%d orientations" % (count, npts))
                prog.setFraction(float(count) / npts)
                count += 1
                if prog.stopped():
                    return None
        return od
コード例 #51
0
ファイル: tsl.py プロジェクト: song2001/OOF2
    def _read(self, tslfile, prog):
        data, hexgrid = self.readData(tslfile, prog)
        npts = len(data)
        rows = list(getrows(data))  # sorts data
        if hexgrid is None:
            # readData didn't set hexgrid.  The grid is hexagonal if
            # the first two rows don't start at the same x.
            hexgrid = rows[0][0].position[0] != rows[1][0].position[0]

        if hexgrid:
            # Throw out every other row.
            reporter.warn("Converting hexagonal lattice to rectangular"
                          " by discarding alternate rows.")
            rows = rows[::2]  # discard odd numbered rows

        nx = len(rows[0])
        ny = len(rows)
        count = 0
        for row in rows:
            count += 1
            if len(row) != nx:
                raise ooferror.ErrUserError(
                    "Orientation map data appears to be incomplete.\n"
                    "len(row 0)=%d len(row %d)=%d" % (nx, count, len(row)))

        # TSL puts the origin at the top left, so it's using a left
        # handed coordinate system!  If flip_y==True, fix that.  Also,
        # make sure there are no negative x or y values.
        ymax = rows[-1][0].position[1]
        ymin = rows[0][0].position[1]
        xmax = rows[0][-1].position[0]
        xmin = rows[0][0].position[0]
        for row in rows:
            for point in row:
                if self.flip_x:
                    point.position[0] = xmax - point.position[0]
                else:
                    point.position[0] = point.position[0] - xmin
                if self.flip_y:
                    point.position[1] = ymax - point.position[1]
                else:
                    point.position[1] = point.position[1] - ymin

        # If flipped, the rows are still ordered top to bottom, but
        # the coordinates increase bottom to top.

        # pixel size
        dx = abs(rows[0][1].position[0] - rows[0][0].position[0])
        dy = abs(rows[0][0].position[1] - rows[1][0].position[1])
        pxlsize = primitives.Point(dx, dy)

        width = abs(rows[0][0].position[0] - rows[0][-1].position[0])
        height = abs(rows[0][0].position[1] - rows[-1][0].position[1])
        # If we assume that the points are in the centers of the
        # pixels, then the actual physical size is one pixel bigger
        # than the range of the xy values.
        size = primitives.Point(width, height) + pxlsize

        od = orientmapdata.OrientMap(primitives.iPoint(nx, ny), size)
        prog.setMessage("%d/%d orientations" % (0, npts))
        count = 0
        for row in rows:
            for datum in row:
                ij = primitives.iPoint(
                    int(round(datum.position[0] / pxlsize[0])),
                    int(round(datum.position[1] / pxlsize[1])))
                try:
                    self.phaselists[datum.phasename].append(ij)
                except KeyError:
                    self.phaselists[datum.phasename] = [ij]
                self.set_angle(od, ij, datum.euler())
                prog.setMessage("%d/%d orientations" % (count, npts))
                prog.setFraction(float(count) / npts)
                count += 1
                if prog.stopped():

                    return None
        prog.finish()
        return od
コード例 #52
0
ファイル: findboundaries.py プロジェクト: anilkunwar/OOF2
imageGeoFilter.SetInput(indexedImage)
imageGeoFilter.SetExtent(imageBounds)
imagePoints = imageGeoFilter.GetOutput()
imagePoints.Update()

# needed to calulate normal and area
polygon = vtk.vtkPolygon()
triangle = vtk.vtkTriangle()
normal = [0.0,0.0,0.0]
pt=[0.0,0.0,0.0]

# loop over voxels and add faces that border different pixel groups to polydata
for i in xrange(indexedImage.GetNumberOfCells()):
    voxel = indexedImage.GetCell(i)
    p = voxel.GetPoints().GetPoint(0)
    point = primitives.iPoint(p[0],p[1],p[2])
    value = indexedImage.GetScalarComponentAsFloat(point[0],point[1],point[2],0)
    for j in xrange(6):
        point2 = point+dirs[j]
        if point2[0] >= imageBounds[0] and point2[0] <= imageBounds[1]-1 and point2[1] >= imageBounds[2] and point2[1] <= imageBounds[3]-1 and point2[2] >= imageBounds[4] and point2[2] <= imageBounds[5]-1:
            value2 = indexedImage.GetScalarComponentAsFloat(point2[0],point2[1],point2[2],0)
            if value2 != value:
                # only add face for the given value, so that we don't
                # get double faces and so that the normal points
                # outward.
                face=voxel.GetFace(j)
                quadpoints = vtk.vtkPoints()
                # We have to explicity make the quad because, very annoyingly,
                # the order of points in the voxels and pixels returned by
                # vtkImageData are not compatible with the quads used for
                # polydata.