Commit 3a906aa240f11aeaa716df8ad345a3cc40b5314e
1 parent
4e527a1a
Exists in
vti
Reading vti
Showing
3 changed files
with
80 additions
and
2 deletions
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invesalius/control.py
| @@ -33,6 +33,7 @@ import data.volume as volume | @@ -33,6 +33,7 @@ import data.volume as volume | ||
| 33 | import gui.dialogs as dialog | 33 | import gui.dialogs as dialog |
| 34 | import project as prj | 34 | import project as prj |
| 35 | import reader.analyze_reader as analyze | 35 | import reader.analyze_reader as analyze |
| 36 | +import reader.vtk_reader as vtk_reader | ||
| 36 | import reader.dicom_grouper as dg | 37 | import reader.dicom_grouper as dg |
| 37 | import reader.dicom_reader as dcm | 38 | import reader.dicom_reader as dcm |
| 38 | import session as ses | 39 | import session as ses |
| @@ -351,8 +352,12 @@ class Controller(): | @@ -351,8 +352,12 @@ class Controller(): | ||
| 351 | self.CreateAnalyzeProject(imagedata) | 352 | self.CreateAnalyzeProject(imagedata) |
| 352 | # OPTION 3: Nothing... | 353 | # OPTION 3: Nothing... |
| 353 | else: | 354 | else: |
| 354 | - utils.debug("No medical images found on given directory") | ||
| 355 | - return | 355 | + imagedata = vtk_reader.ReadDirectory(directory) |
| 356 | + if imagedata: | ||
| 357 | + self.CreateVTKProject(imagedata) | ||
| 358 | + else: | ||
| 359 | + utils.debug("No medical images found on given directory") | ||
| 360 | + return | ||
| 356 | self.LoadProject() | 361 | self.LoadProject() |
| 357 | Publisher.sendMessage("Enable state project", True) | 362 | Publisher.sendMessage("Enable state project", True) |
| 358 | 363 | ||
| @@ -414,6 +419,44 @@ class Controller(): | @@ -414,6 +419,44 @@ class Controller(): | ||
| 414 | 419 | ||
| 415 | Publisher.sendMessage('End busy cursor') | 420 | Publisher.sendMessage('End busy cursor') |
| 416 | 421 | ||
| 422 | + def CreateVTKProject(self, imagedata): | ||
| 423 | + proj = prj.Project() | ||
| 424 | + proj.imagedata = None | ||
| 425 | + proj.name = _("Untitled") | ||
| 426 | + proj.SetAcquisitionModality("CT") | ||
| 427 | + #TODO: Verify if all Analyse are in AXIAL orientation | ||
| 428 | + | ||
| 429 | + # To get Z, X, Y (used by InVesaliu), not X, Y, Z | ||
| 430 | + | ||
| 431 | + proj.threshold_range = imagedata.GetScalarRange() | ||
| 432 | + proj.window = proj.threshold_range[1] - proj.threshold_range[0] | ||
| 433 | + proj.level = (0.5 * (proj.threshold_range[1] + proj.threshold_range[0])) | ||
| 434 | + proj.spacing = imagedata.GetSpacing() | ||
| 435 | + proj.matrix_shape = imagedata.GetDimensions()[::-1] | ||
| 436 | + proj.original_orientation = const.AXIAL | ||
| 437 | + | ||
| 438 | + matrix, matrix_filename = image_utils.vtk2mmap(imagedata) | ||
| 439 | + proj.matrix_dtype = matrix.dtype.name | ||
| 440 | + proj.matrix_filename = matrix_filename | ||
| 441 | + | ||
| 442 | + self.Slice = sl.Slice() | ||
| 443 | + self.Slice.matrix = matrix | ||
| 444 | + self.Slice.matrix_filename = matrix_filename | ||
| 445 | + | ||
| 446 | + self.Slice.window_level = proj.level | ||
| 447 | + self.Slice.window_width = proj.window | ||
| 448 | + self.Slice.spacing = proj.spacing | ||
| 449 | + | ||
| 450 | + session = ses.Session() | ||
| 451 | + filename = proj.name+".inv3" | ||
| 452 | + | ||
| 453 | + filename = filename.replace("/", "") #Fix problem case other/Skull_DICOM | ||
| 454 | + | ||
| 455 | + dirpath = session.CreateProject(filename) | ||
| 456 | + | ||
| 457 | + Publisher.sendMessage('Update threshold limits list', | ||
| 458 | + proj.threshold_range) | ||
| 459 | + | ||
| 417 | def CreateAnalyzeProject(self, imagedata): | 460 | def CreateAnalyzeProject(self, imagedata): |
| 418 | header = imagedata.get_header() | 461 | header = imagedata.get_header() |
| 419 | proj = prj.Project() | 462 | proj = prj.Project() |
invesalius/data/imagedata_utils.py
| @@ -493,6 +493,16 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage): | @@ -493,6 +493,16 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage): | ||
| 493 | 493 | ||
| 494 | return matrix, scalar_range, temp_file | 494 | return matrix, scalar_range, temp_file |
| 495 | 495 | ||
| 496 | +def vtk2mmap(imagedata): | ||
| 497 | + temp_file = tempfile.mktemp() | ||
| 498 | + shape = imagedata.GetDimensions()[::-1] | ||
| 499 | + array = numpy_support.vtk_to_numpy(imagedata.GetPointData().GetScalars()) | ||
| 500 | + array.shape = shape | ||
| 501 | + matrix = numpy.memmap(temp_file, mode='w+', dtype='int16', shape=shape) | ||
| 502 | + matrix[:] = array | ||
| 503 | + matrix.flush() | ||
| 504 | + return matrix, temp_file | ||
| 505 | + | ||
| 496 | def analyze2mmap(analyze): | 506 | def analyze2mmap(analyze): |
| 497 | data = analyze.get_data() | 507 | data = analyze.get_data() |
| 498 | header = analyze.get_header() | 508 | header = analyze.get_header() |
| @@ -0,0 +1,25 @@ | @@ -0,0 +1,25 @@ | ||
| 1 | +import os | ||
| 2 | +import multiprocessing | ||
| 3 | +import tempfile | ||
| 4 | + | ||
| 5 | +import vtk | ||
| 6 | + | ||
| 7 | +def ReadVTK(filename): | ||
| 8 | + r = vtk.vtkXMLImageDataReader() | ||
| 9 | + r.SetFileName(filename) | ||
| 10 | + r.Update() | ||
| 11 | + | ||
| 12 | + return r.GetOutput() | ||
| 13 | + | ||
| 14 | +def ReadDirectory(dir_): | ||
| 15 | + """ | ||
| 16 | + Looking for analyze files in the given directory | ||
| 17 | + """ | ||
| 18 | + imagedata = None | ||
| 19 | + for root, sub_folders, files in os.walk(dir_): | ||
| 20 | + for file in files: | ||
| 21 | + if file.split(".")[-1] == "vti": | ||
| 22 | + filename = os.path.join(root,file) | ||
| 23 | + imagedata = ReadVTK(filename) | ||
| 24 | + return imagedata | ||
| 25 | + return imagedata |