Fix bug in 3d view; add test data

CBICA · Dec 9, 2024 · 6f81fd7 · 6f81fd7
1 parent 0576ff5
commit 6f81fd7
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Showing 31 changed files with 27 additions and 11 deletions.
diff --git a/src/Image_Processing/DTI/qsiprep b/src/Image_Processing/DTI/qsiprep
diff --git a/src/Image_Processing/fMRI/fmriprep b/src/Image_Processing/fMRI/fmriprep
diff --git a/src/Image_Processing/fMRI/xcp_d b/src/Image_Processing/fMRI/xcp_d
diff --git a/src/Image_Processing/sMRI/DLICV b/src/Image_Processing/sMRI/DLICV
diff --git a/src/Image_Processing/sMRI/DLMUSE b/src/Image_Processing/sMRI/DLMUSE
diff --git a/src/Machine_Learning/spare_score b/src/Machine_Learning/spare_score
diff --git a/src/viewer/pages/plot_sMRI_vars_study.py b/src/viewer/pages/plot_sMRI_vars_study.py
@@ -361,13 +361,14 @@ def show_img() -> None:
         for i, tmp_orient in enumerate(list_orient):
             with blocks[i]:
                 ind_view = utilni.img_views.index(tmp_orient)
+                size_auto = True
                 if not st.session_state.mriview_var["show_overlay"]:
                     utilst.show_img3D(
-                        img, ind_view, mask_bounds[ind_view, :], tmp_orient
+                        img, ind_view, mask_bounds[ind_view, :], tmp_orient, size_auto
                     )
                 else:
                     utilst.show_img3D(
-                        img_masked, ind_view, mask_bounds[ind_view, :], tmp_orient
+                        img_masked, ind_view, mask_bounds[ind_view, :], tmp_orient, size_auto
                     )
 
 

diff --git a/src/viewer/pages/process_sMRI_DLMUSE.py b/src/viewer/pages/process_sMRI_DLMUSE.py
@@ -329,7 +329,7 @@ def panel_view() -> None:
                                 ind_view,
                                 mask_bounds[ind_view, :],
                                 tmp_orient,
-                                size_auto = True
+                                size_auto
                             )
 
 

diff --git a/src/viewer/pages/process_sMRI_DLWMLS.py b/src/viewer/pages/process_sMRI_DLWMLS.py
@@ -234,13 +234,14 @@ def panel_view() -> None:
             ):
                 with blocks[i]:
                     ind_view = utilni.img_views.index(tmp_orient)
+                    size_auto = True
                     if is_show_overlay is False:
                         utilst.show_img3D(
-                            img, ind_view, mask_bounds[ind_view, :], tmp_orient
+                            img, ind_view, mask_bounds[ind_view, :], tmp_orient, size_auto
                         )
                     else:
                         utilst.show_img3D(
-                            img_masked, ind_view, mask_bounds[ind_view, :], tmp_orient
+                            img_masked, ind_view, mask_bounds[ind_view, :], tmp_orient, size_auto
                         )
 
 

diff --git a/...fti/IXI_smallset/IXI012-HH-1211_T1.nii.gz → ...ata/nifti/IXI_n1/IXI012-HH-1211_T1.nii.gz b/...fti/IXI_smallset/IXI012-HH-1211_T1.nii.gz → ...ata/nifti/IXI_n1/IXI012-HH-1211_T1.nii.gz
diff --git a/test_data/nifti/IXI_n1/IXI_Demog_n1.csv b/test_data/nifti/IXI_n1/IXI_Demog_n1.csv
@@ -0,0 +1,2 @@
+MRID,Age,Sex
+IXI012-HH-1211,38.78,M
diff --git a/...fti/IXI_smallset/IXI015-HH-1258_T1.nii.gz → ...gularname/IXI015-HH-1258-series003.nii.gz b/...fti/IXI_smallset/IXI015-HH-1258_T1.nii.gz → ...gularname/IXI015-HH-1258-series003.nii.gz
diff --git a/test_data/nifti/IXI_n1_irregularname/IXI_Demog_n2.csv b/test_data/nifti/IXI_n1_irregularname/IXI_Demog_n2.csv
@@ -0,0 +1,2 @@
+MRID,Age,Sex
+IXI015-HH-1258-series003,24.28,M
diff --git a/...mallset/Nifti/T1/IXI012-HH-1211_T1.nii.gz → ...ata/nifti/IXI_n2/IXI012-HH-1211_T1.nii.gz b/...mallset/Nifti/T1/IXI012-HH-1211_T1.nii.gz → ...ata/nifti/IXI_n2/IXI012-HH-1211_T1.nii.gz
diff --git a/...mallset/Nifti/T1/IXI015-HH-1258_T1.nii.gz → ...ata/nifti/IXI_n2/IXI015-HH-1258_T1.nii.gz b/...mallset/Nifti/T1/IXI015-HH-1258_T1.nii.gz → ...ata/nifti/IXI_n2/IXI015-HH-1258_T1.nii.gz
diff --git a/test_data/nifti/IXI_Demog_n2.csv → test_data/nifti/IXI_n2/IXI_Demog_n2.csv b/test_data/nifti/IXI_Demog_n2.csv → test_data/nifti/IXI_n2/IXI_Demog_n2.csv
diff --git a/test_data/nifti/IXI_n2_irregularname/IXI012-HH-1211_scan1-mprage.nii.gz b/test_data/nifti/IXI_n2_irregularname/IXI012-HH-1211_scan1-mprage.nii.gz
diff --git a/test_data/nifti/IXI_n2_irregularname/IXI015-HH-1258-series003.nii.gz b/test_data/nifti/IXI_n2_irregularname/IXI015-HH-1258-series003.nii.gz
diff --git a/test_data/nifti/IXI_n2_irregularname/IXI_Demog_n2.csv b/test_data/nifti/IXI_n2_irregularname/IXI_Demog_n2.csv
@@ -0,0 +1,3 @@
+MRID,Age,Sex
+IXI012-HH-1211_scan1-mprage,38.78,M
+IXI015-HH-1258-series003,24.28,M
diff --git a/test_data/processed/IXI_n1/DLMUSE/DLMUSE_Volumes.csv b/test_data/processed/IXI_n1/DLMUSE/DLMUSE_Volumes.csv
@@ -0,0 +1,2 @@
+MRID,702,701,600,601,604,606,607,613,614,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,4,11,23,30,31,32,35,36,37,38,39,40,41,47,48,49,50,51,52,55,56,57,58,59,60,61,62,71,72,73,75,76,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,100,101,102,103,104,105,106,107,108,109,112,113,114,115,116,117,118,119,120,121,122,123,124,125,128,129,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207
+IXI012-HH-1211,1652136.0,1521560.0,129000.0,832544.0,645952.0,408792.0,319848.0,412952.0,312136.0,13968.0,174904.0,63984.0,488440.0,44456.0,165152.0,239760.0,277288.0,19192.0,81864.0,31456.0,241872.0,23208.0,83104.0,122800.0,138848.0,10344.0,82240.0,32528.0,246568.0,21248.0,82048.0,116960.0,138440.0,6016.0,18928.0,18144.0,12760.0,239080.0,249360.0,44456.0,100824.0,64328.0,117352.0,122408.0,137760.0,139528.0,9216.0,9208.0,6272.0,117128.0,124744.0,23208.0,50704.0,32400.0,58288.0,64512.0,68936.0,69912.0,9712.0,8936.0,6488.0,121952.0,124616.0,21248.0,50120.0,31928.0,59064.0,57896.0,68824.0,69616.0,26144.0,14016.0,133720.0,46496.0,18704.0,30632.0,13824.0,11248.0,47032.0,42544.0,88552.0,28800.0,18768.0,107680.0,11312.0,13112.0,6840.0,65088.0,22520.0,9568.0,16424.0,6784.0,5808.0,24120.0,20776.0,43440.0,14848.0,9984.0,53016.0,5936.0,13032.0,7176.0,68632.0,23976.0,9136.0,14208.0,7040.0,5440.0,22912.0,21768.0,45112.0,13952.0,8784.0,54664.0,5376.0,1472.0,1360.0,416.0,432.0,1144.0,1176.0,23872.0,3144.0,2840.0,65704.0,65344.0,16536.0,16520.0,5448.0,4856.0,216.0,200.0,5800.0,10144.0,1632.0,1600.0,4520.0,4344.0,8936.0,9208.0,5056.0,5488.0,5072.0,1992.0,3736.0,728.0,800.0,124616.0,124744.0,31928.0,32400.0,57896.0,64512.0,69616.0,69912.0,456.0,640.0,3712.0,3272.0,2320.0,2360.0,13968.0,4808.0,6280.0,4640.0,4424.0,2248.0,1736.0,11560.0,9552.0,4128.0,4568.0,4968.0,4600.0,7000.0,6568.0,2808.0,2744.0,2016.0,2008.0,3664.0,3904.0,8784.0,9984.0,2656.0,2864.0,7936.0,9152.0,15816.0,14520.0,10640.0,9640.0,2344.0,2584.0,5192.0,5728.0,2688.0,2272.0,23272.0,23048.0,6576.0,7360.0,5080.0,5672.0,712.0,864.0,3176.0,3600.0,7952.0,5760.0,17696.0,18152.0,4352.0,4464.0,5440.0,5808.0,3712.0,3896.0,1888.0,1840.0,4208.0,4416.0,13240.0,13984.0,4232.0,4040.0,2536.0,2416.0,2152.0,2960.0,13336.0,13640.0,3360.0,3120.0,1880.0,2128.0,14328.0,13472.0,1832.0,1984.0,1592.0,1832.0,18336.0,15496.0,5912.0,6192.0,10912.0,10312.0,4048.0,3144.0,9304.0,9936.0,8832.0,8928.0,12320.0,11416.0,3432.0,3432.0,1664.0,1824.0
diff --git a/...et/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz → ...n1/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz b/...et/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz → ...n1/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz
diff --git a/...IXI_smallset/MLScores/DLMUSE+MLScores.csv → ...essed/IXI_n1/MLScores/DLMUSE+MLScores.csv b/...IXI_smallset/MLScores/DLMUSE+MLScores.csv → ...essed/IXI_n1/MLScores/DLMUSE+MLScores.csv
diff --git a/test_data/processed/IXI_n1/Nifti/T1/IXI012-HH-1211_T1.nii.gz b/test_data/processed/IXI_n1/Nifti/T1/IXI012-HH-1211_T1.nii.gz
diff --git a/test_data/processed/IXI_n1/lists/Demog.csv b/test_data/processed/IXI_n1/lists/Demog.csv
@@ -0,0 +1,2 @@
+MRID,Age,Sex
+IXI012-HH-1211,38.78,M
diff --git a/...ed/IXI_smallset/DLMUSE/DLMUSE_Volumes.csv → ...rocessed/IXI_n2/DLMUSE/DLMUSE_Volumes.csv b/...ed/IXI_smallset/DLMUSE/DLMUSE_Volumes.csv → ...rocessed/IXI_n2/DLMUSE/DLMUSE_Volumes.csv
diff --git a/test_data/processed/IXI_n2/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz b/test_data/processed/IXI_n2/DLMUSE/IXI012-HH-1211_T1_DLMUSE.nii.gz
diff --git a/...et/DLMUSE/IXI015-HH-1258_T1_DLMUSE.nii.gz → ...n2/DLMUSE/IXI015-HH-1258_T1_DLMUSE.nii.gz b/...et/DLMUSE/IXI015-HH-1258_T1_DLMUSE.nii.gz → ...n2/DLMUSE/IXI015-HH-1258_T1_DLMUSE.nii.gz
diff --git a/test_data/processed/IXI_n2/MLScores/DLMUSE+MLScores.csv b/test_data/processed/IXI_n2/MLScores/DLMUSE+MLScores.csv
diff --git a/test_data/processed/IXI_n2/Nifti/T1/IXI012-HH-1211_T1.nii.gz b/test_data/processed/IXI_n2/Nifti/T1/IXI012-HH-1211_T1.nii.gz
diff --git a/test_data/processed/IXI_n2/Nifti/T1/IXI015-HH-1258_T1.nii.gz b/test_data/processed/IXI_n2/Nifti/T1/IXI015-HH-1258_T1.nii.gz
diff --git a/...ta/processed/IXI_smallset/lists/Demog.csv → test_data/processed/IXI_n2/lists/Demog.csv b/...ta/processed/IXI_smallset/lists/Demog.csv → test_data/processed/IXI_n2/lists/Demog.csv
+14 −6		docs/quickstart.rst
+2 −2		qsiprep/interfaces/images.py
+1 −1		.pre-commit-config.yaml
+13 −0		CHANGES.rst
+8 −8		Dockerfile
+2 −2		env.yml
+2 −2		fmriprep/workflows/bold/resampling.py
+5 −5		pyproject.toml
+80 −34		requirements.txt
+35 −0		.gitattributes
+17 −0		.github/workflows/pre-commit.yml
+31 −30		.github/workflows/python-publish.yml
+5 −1		.gitignore
+19 −0		.pre-commit-config.yaml
+35 −0		DLICV/.gitattributes
+5 −0		DLICV/README.md
+0 −1		DLICV/VERSION
+339 −65		DLICV/__main__.py
+0 −63		DLICV/compute_icv.py
+11 −0		DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json
+18,078 −0		DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json
+434 −0		DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json
+9,062 −0		DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json
+11,242 −0		DLICV/nnunet_raw/Dataset901_Task901_dlicv/datalist.json
+11 −0		DLICV/nnunet_raw/Dataset901_Task901_dlicv/dataset.json
+35 −0		DLICV/src/.gitattributes
+41 −0		DLICV/utils.py
+1 −1		Dockerfile
+0 −2		MANIFEST.in
+13 −92		README.md
+0 −2		requirements-dev.txt
+0 −3		requirements-test.txt
+4 −2		requirements.txt
+42 −0		setup.cfg
+22 −32		setup.py
+0 −0		tests/__init__.py
+34 −33		tests/test_main.py
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		MRID,702,701,600,601,604,606,607,613,614,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,4,11,23,30,31,32,35,36,37,38,39,40,41,47,48,49,50,51,52,55,56,57,58,59,60,61,62,71,72,73,75,76,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,100,101,102,103,104,105,106,107,108,109,112,113,114,115,116,117,118,119,120,121,122,123,124,125,128,129,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207
		IXI012-HH-1211,1652136.0,1521560.0,129000.0,832544.0,645952.0,408792.0,319848.0,412952.0,312136.0,13968.0,174904.0,63984.0,488440.0,44456.0,165152.0,239760.0,277288.0,19192.0,81864.0,31456.0,241872.0,23208.0,83104.0,122800.0,138848.0,10344.0,82240.0,32528.0,246568.0,21248.0,82048.0,116960.0,138440.0,6016.0,18928.0,18144.0,12760.0,239080.0,249360.0,44456.0,100824.0,64328.0,117352.0,122408.0,137760.0,139528.0,9216.0,9208.0,6272.0,117128.0,124744.0,23208.0,50704.0,32400.0,58288.0,64512.0,68936.0,69912.0,9712.0,8936.0,6488.0,121952.0,124616.0,21248.0,50120.0,31928.0,59064.0,57896.0,68824.0,69616.0,26144.0,14016.0,133720.0,46496.0,18704.0,30632.0,13824.0,11248.0,47032.0,42544.0,88552.0,28800.0,18768.0,107680.0,11312.0,13112.0,6840.0,65088.0,22520.0,9568.0,16424.0,6784.0,5808.0,24120.0,20776.0,43440.0,14848.0,9984.0,53016.0,5936.0,13032.0,7176.0,68632.0,23976.0,9136.0,14208.0,7040.0,5440.0,22912.0,21768.0,45112.0,13952.0,8784.0,54664.0,5376.0,1472.0,1360.0,416.0,432.0,1144.0,1176.0,23872.0,3144.0,2840.0,65704.0,65344.0,16536.0,16520.0,5448.0,4856.0,216.0,200.0,5800.0,10144.0,1632.0,1600.0,4520.0,4344.0,8936.0,9208.0,5056.0,5488.0,5072.0,1992.0,3736.0,728.0,800.0,124616.0,124744.0,31928.0,32400.0,57896.0,64512.0,69616.0,69912.0,456.0,640.0,3712.0,3272.0,2320.0,2360.0,13968.0,4808.0,6280.0,4640.0,4424.0,2248.0,1736.0,11560.0,9552.0,4128.0,4568.0,4968.0,4600.0,7000.0,6568.0,2808.0,2744.0,2016.0,2008.0,3664.0,3904.0,8784.0,9984.0,2656.0,2864.0,7936.0,9152.0,15816.0,14520.0,10640.0,9640.0,2344.0,2584.0,5192.0,5728.0,2688.0,2272.0,23272.0,23048.0,6576.0,7360.0,5080.0,5672.0,712.0,864.0,3176.0,3600.0,7952.0,5760.0,17696.0,18152.0,4352.0,4464.0,5440.0,5808.0,3712.0,3896.0,1888.0,1840.0,4208.0,4416.0,13240.0,13984.0,4232.0,4040.0,2536.0,2416.0,2152.0,2960.0,13336.0,13640.0,3360.0,3120.0,1880.0,2128.0,14328.0,13472.0,1832.0,1984.0,1592.0,1832.0,18336.0,15496.0,5912.0,6192.0,10912.0,10312.0,4048.0,3144.0,9304.0,9936.0,8832.0,8928.0,12320.0,11416.0,3432.0,3432.0,1664.0,1824.0