BoyaWu10 commited on
Commit
19cfb69
1 Parent(s): a2f2ef1

crop foreground (#4)

Browse files

- add crop foreground (be79dc591f01372be453d63eed50d430485a61be)

app.py CHANGED
@@ -296,8 +296,17 @@ with col2:
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  img_nii = None
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  if st.session_state.preds_3D_ori is not None and st.session_state.data_item is not None:
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  meta_dict = st.session_state.data_item['meta']
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- pred_array = st.session_state.preds_3D_ori.transpose(2, 1, 0)
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- img_nii = nib.Nifti1Image(pred_array, affine=meta_dict['affine'])
 
 
 
 
 
 
 
 
 
301
 
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  with tempfile.NamedTemporaryFile(suffix=".nii.gz") as tmpfile:
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  nib.save(img_nii, tmpfile.name)
@@ -323,9 +332,6 @@ with col3:
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  st.session_state.running = True
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  st.rerun()
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- # if len(st.session_state.points) > 0:
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- # st.write(st.session_state.points)
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-
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  if st.session_state.running:
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  st.session_state.running = False
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  with st.status("Running...", expanded=False) as status:
 
296
  img_nii = None
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  if st.session_state.preds_3D_ori is not None and st.session_state.data_item is not None:
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  meta_dict = st.session_state.data_item['meta']
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+ foreground_start_coord = st.session_state.data_item['foreground_start_coord']
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+ foreground_end_coord = st.session_state.data_item['foreground_end_coord']
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+ original_shape = st.session_state.data_item['ori_shape']
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+ pred_array = st.session_state.preds_3D_ori
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+ original_array = np.zeros(original_shape)
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+ original_array[foreground_start_coord[0]:foreground_end_coord[0],
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+ foreground_start_coord[1]:foreground_end_coord[1],
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+ foreground_start_coord[2]:foreground_end_coord[2]] = pred_array
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+
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+ original_array = original_array.transpose(2, 1, 0)
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+ img_nii = nib.Nifti1Image(original_array, affine=meta_dict['affine'])
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311
  with tempfile.NamedTemporaryFile(suffix=".nii.gz") as tmpfile:
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  nib.save(img_nii, tmpfile.name)
 
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  st.session_state.running = True
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  st.rerun()
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  if st.session_state.running:
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  st.session_state.running = False
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  with st.status("Running...", expanded=False) as status:
model/data_process/__pycache__/demo_data_process.cpython-39.pyc CHANGED
Binary files a/model/data_process/__pycache__/demo_data_process.cpython-39.pyc and b/model/data_process/__pycache__/demo_data_process.cpython-39.pyc differ
 
model/data_process/demo_data_process.py CHANGED
@@ -60,7 +60,7 @@ def process_ct_gt(case_path, spatial_size=(32,256,256)):
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  DimTranspose(keys=["image"]),
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  MinMaxNormalization(),
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  transforms.SpatialPadd(keys=["image"], spatial_size=spatial_size, mode='constant'),
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- # transforms.CropForegroundd(keys=["image"], source_key="image"),
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  transforms.ToTensord(keys=["image"]),
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  ]
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  )
@@ -81,12 +81,14 @@ def process_ct_gt(case_path, spatial_size=(32,256,256)):
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  ct_voxel_ndarray = np.array(ct_voxel_ndarray).squeeze()
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  ct_voxel_ndarray = np.expand_dims(ct_voxel_ndarray, axis=0)
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  item['image'] = ct_voxel_ndarray
 
84
 
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  # transform
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  item = transform(item)
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  item_zoom_out = zoom_out_transform(item)
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  item['zoom_out_image'] = item_zoom_out['image']
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-
 
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  item_z = z_transform(item)
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  item['z_image'] = item_z['image']
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  item['meta'] = meta_tensor_dict
 
60
  DimTranspose(keys=["image"]),
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  MinMaxNormalization(),
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  transforms.SpatialPadd(keys=["image"], spatial_size=spatial_size, mode='constant'),
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+ transforms.CropForegroundd(keys=["image"], source_key="image"),
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  transforms.ToTensord(keys=["image"]),
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  ]
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  )
 
81
  ct_voxel_ndarray = np.array(ct_voxel_ndarray).squeeze()
82
  ct_voxel_ndarray = np.expand_dims(ct_voxel_ndarray, axis=0)
83
  item['image'] = ct_voxel_ndarray
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+ ori_shape = np.swapaxes(ct_voxel_ndarray, -1, -3).shape[1:]
85
 
86
  # transform
87
  item = transform(item)
88
  item_zoom_out = zoom_out_transform(item)
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  item['zoom_out_image'] = item_zoom_out['image']
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+ item['ori_shape'] = ori_shape
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+
92
  item_z = z_transform(item)
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  item['z_image'] = item_z['image']
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  item['meta'] = meta_tensor_dict