Download as
Browse Code »

Commit d498a62eda097803ac743abd7fe5cb6042cfad8f

Authored by Thiago Franco de Moraes
1 parent 10ed1e32
Exists in master

Added option to apply ww&wl

Showing 2 changed files with 32 additions and 2 deletions   Show diff stats
invesalius/gui/brain_seg_dialog.py
  Diff comments   View file @d498a62
... ... @@ -81,6 +81,8 @@ class BrainSegmenterDialog(wx.Dialog):
81 81 self.txt_threshold.SetMinClientSize((w, -1))
82 82 self.chk_new_mask = wx.CheckBox(self, wx.ID_ANY, _("Create new mask"))
83 83 self.chk_new_mask.SetValue(True)
  84 + self.chk_apply_wwwl = wx.CheckBox(self, wx.ID_ANY, _("Apply WW&WL"))
  85 + self.chk_apply_wwwl.SetValue(False)
84 86 self.progress = wx.Gauge(self, -1)
85 87 self.lbl_progress_caption = wx.StaticText(self, -1, _("Elapsed time:"))
86 88 self.lbl_time = wx.StaticText(self, -1, _("00:00:00"))
... ... @@ -120,6 +122,7 @@ class BrainSegmenterDialog(wx.Dialog):
120 122 )
121 123 sizer_3.Add(self.txt_threshold, 0, wx.ALL, 5)
122 124 main_sizer.Add(sizer_3, 0, wx.EXPAND, 0)
  125 + main_sizer.Add(self.chk_apply_wwwl, 0, wx.EXPAND | wx.ALL, 5)
123 126 main_sizer.Add(self.chk_new_mask, 0, wx.EXPAND | wx.ALL, 5)
124 127 main_sizer.Add(self.progress, 0, wx.EXPAND | wx.ALL, 5)
125 128 time_sizer = wx.BoxSizer(wx.HORIZONTAL)
... ... @@ -216,6 +219,7 @@ class BrainSegmenterDialog(wx.Dialog):
216 219 device_id = self.plaidml_devices[self.cb_devices.GetValue()]
217 220 except (KeyError, AttributeError):
218 221 device_id = "llvm_cpu.0"
  222 + apply_wwwl = self.chk_apply_wwwl.GetValue()
219 223 create_new_mask = self.chk_new_mask.GetValue()
220 224 use_gpu = self.chk_use_gpu.GetValue()
221 225 prob_threshold = self.sld_threshold.GetValue() / 100.0
... ... @@ -224,8 +228,11 @@ class BrainSegmenterDialog(wx.Dialog):
224 228 self.btn_segment.Disable()
225 229 self.chk_new_mask.Disable()
226 230  
  231 + window_width = slc.Slice().window_width
  232 + window_level = slc.Slice().window_level
  233 +
227 234 try:
228   - self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu)
  235 + self.ps = segment.SegmentProcess(image, create_new_mask, backend, device_id, use_gpu, apply_wwwl, window_width, window_level)
229 236 self.ps.start()
230 237 except (multiprocessing.ProcessError, OSError, ValueError) as err:
231 238 self.OnStop(None)
... ...
invesalius/segmentation/brain/segment.py
  Diff comments   View file @d498a62
... ... @@ -20,6 +20,17 @@ SIZE = 48
20 20 OVERLAP = SIZE // 2 + 1
21 21  
22 22  
  23 +def get_LUT_value(data, window, level):
  24 + shape = data.shape
  25 + data_ = data.ravel()
  26 + data = np.piecewise(data_,
  27 + [data_ <= (level - 0.5 - (window-1)/2),
  28 + data_ > (level - 0.5 + (window-1)/2)],
  29 + [0, window, lambda data_: ((data_ - (level - 0.5))/(window-1) + 0.5)*(window)])
  30 + data.shape = shape
  31 + return data
  32 +
  33 +
23 34 def gen_patches(image, patch_size, overlap):
24 35 sz, sy, sx = image.shape
25 36 i_cuts = list(
... ... @@ -63,6 +74,8 @@ def brain_segment(image, probability_array, comm_array):
63 74 model = keras.models.model_from_json(json_file.read())
64 75 model.load_weights(str(folder.joinpath("model.h5")))
65 76 model.compile("Adam", "binary_crossentropy")
  77 +
  78 + keras.utils.plot_model(model, "model.png", show_shapes=True, show_layer_names=True)
66 79  
67 80 image = imagedata_utils.image_normalize(image, 0.0, 1.0, output_dtype=np.float32)
68 81 sums = np.zeros_like(image)
... ... @@ -80,7 +93,7 @@ def brain_segment(image, probability_array, comm_array):
80 93  
81 94 ctx = multiprocessing.get_context('spawn')
82 95 class SegmentProcess(ctx.Process):
83   - def __init__(self, image, create_new_mask, backend, device_id, use_gpu):
  96 + def __init__(self, image, create_new_mask, backend, device_id, use_gpu, apply_wwwl=False, window_width=255, window_level=127):
84 97 multiprocessing.Process.__init__(self)
85 98  
86 99 self._image_filename = image.filename
... ... @@ -102,6 +115,10 @@ class SegmentProcess(ctx.Process):
102 115 self.device_id = device_id
103 116 self.use_gpu = use_gpu
104 117  
  118 + self.apply_wwwl = apply_wwwl
  119 + self.window_width = window_width
  120 + self.window_level = window_level
  121 +
105 122 self._pconn, self._cconn = multiprocessing.Pipe()
106 123 self._exception = None
107 124  
... ... @@ -122,6 +139,12 @@ class SegmentProcess(ctx.Process):
122 139 shape=self._image_shape,
123 140 mode="r",
124 141 )
  142 +
  143 + print(image.min(), image.max())
  144 + if self.apply_segment_threshold:
  145 + print("Applying window level")
  146 + image = get_LUT_value(image, self.window_width, self.window_level)
  147 +
125 148 probability_array = np.memmap(
126 149 self._prob_array_filename,
127 150 dtype=np.float32,
... ...