Xuemin3

tests/test_scripts/test_apply_warp.py

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+import warnings
+
+warnings.simplefilter("ignore")
+from ndmg.utils import gen_utils as mgu
+import nibabel as nib
+import numpy as np
+import nilearn.image as nl
+import os
+import os.path as op
+import nilearn.image as nl
+import pytest
+from ndmg.utils.reg_utils import apply_warp
+
+
+from ndmg.utils import reg_utils as rgu
+
+def test_apply_warp(tmp_path):
+    #ref= r"/Users/xueminzhu/ndmg_outputs/anat/preproc/t1w_brain_nores.nii.gz"
+    #trainout= r"/Users/xueminzhu/ndmg_outputs/tmp/reg_a/desikan_space-MNI152NLin6_res-2x2x2_reor_RAS_nores_aligned_atlas_skull.nii.gz"
+    #warp=r"/Users/xueminzhu/ndmg_outputs/tmp/reg_a/mni2t1w_warp.nii.gz"
+    #ref_in_path = r"/Users/xueminzhu/ndmg_outputs/anat/preproc/t1w_brain_norse.nii.gz"
+    #inp_in_path= r"/Users/xueminzhu/ndmg_outputs/tmp/reg_a/desikan_space-MNI152NLin6_res-2x2x2_reor_RAS_nores_aligned_atlas_t1w_mni.nii.gz"
+    #out= r"/Users/xueminzhu/ndmg_outputs/tmp/reg_a/desikan_space-MNI152NLin6_res-2x2x2_reor_RAS_nores_aligned_atlas_skull.nii.gz"
+    #warp1=r"/Users/xueminzhu/ndmg_outputs/tmp/reg_a/mni2t1w_warp.nii.gz"
+
+    #make a temporary path#
+    d = tmp_path / "sub"
+    d.mkdir()
+    out_out_cntrl_path = d / "outnii.nii.gz"
+    warp_out_cntrl_path = d/  "warpnii.nii.gz"
+
+    #define correct input data path
+    ref_in_path = '../test_data/inputs/apply_warp/t1w_brain_nores.nii.gz'
+    inp_in_path = '../test_data/inputs/apply_warp/desikan_space-MNI152NLin6_res-2x2x2_reor_RAS_nores_aligned_atlas_t1w_mni.nii.gz'
+    warp_out_cntrl_path_temp = '../test_data/outputs/apply_warp/mni2t1w_warp.nii.gz'
+    out = out_out_cntrl_path
+    warp = warp_out_cntrl_path
+
+    apply_warp(str(ref_in_path),str(inp_in_path),str(out_out_cntrl_path),str(warp_out_cntrl_path))
+
+
+
+    warp_out_cntrl_temp = nib.load(str(warp_out_cntrl_path_temp)).get_fdata()
+
+    warp_out_cntrl = nib.load(str(warp_out_cntrl_path)).get_fdata()
+
+
+    assert np.allclose(warp_out_cntrl_temp,warp_out_cntrl)