dbdicom 0.3.2__py3-none-any.whl → 0.3.4__py3-none-any.whl

dbdicom/sop_classes/mr_image.py

@@ -23,33 +23,54 @@ def pixel_data(ds):
     if [0x2005, 0x100E] in ds: # 'Philips Rescale Slope'
         slope = ds[(0x2005, 0x100E)].value
         intercept = ds[(0x2005, 0x100D)].value
-        array -= intercept
-        array /= slope
+        if (intercept == 0) and (slope == 1): 
+            array = array.astype(np.int16)
+        else:
+            array = array.astype(np.float32)
+            array -= intercept
+            array /= slope
     else:
         slope = float(getattr(ds, 'RescaleSlope', 1)) 
         intercept = float(getattr(ds, 'RescaleIntercept', 0)) 
-        array *= slope
-        array += intercept
+        if (intercept == 0) and (slope == 1): 
+            array = array.astype(np.int16)
+        else:
+            array = array.astype(np.float32)
+            array *= slope
+            array += intercept
     return np.transpose(array)
 
 
 def set_pixel_data(ds, array):
 
+    # Delete 'Philips Rescale Slope'
     if (0x2005, 0x100E) in ds: 
-        del ds[0x2005, 0x100E]  # Delete 'Philips Rescale Slope'
+        del ds[0x2005, 0x100E] 
     if (0x2005, 0x100D) in ds: 
         del ds[0x2005, 0x100D]
 
+    ds.BitsAllocated = 16
+    ds.BitsStored = 16
+    ds.HighBit = 15
+
     # clipping may slow down a lot
-    array = image.clip(array.astype(np.float32))
-    array, slope, intercept = image.scale_to_range(array, ds.BitsAllocated)
-    array = np.transpose(array)
+    #array = image.clip(array.astype(np.float32))
+    array = image.clip(array) # remove nan and infs
+    if array.dtype==np.int16:
+        ds.PixelRepresentation = 1
+        ds.RescaleSlope = 1
+        ds.RescaleIntercept = 0
+    elif array.dtype==np.uint16:
+        ds.PixelRepresentation = 0
+        ds.RescaleSlope = 1
+        ds.RescaleIntercept = 0
+    else:
+        array, slope, intercept = image.scale_to_range(array, ds.BitsStored)
+        ds.PixelRepresentation = 0
+        ds.RescaleSlope = 1 / slope
+        ds.RescaleIntercept = - intercept / slope
 
-    ds.PixelRepresentation = 0
-    ds.RescaleSlope = 1 / slope
-    ds.RescaleIntercept = - intercept / slope
-#        ds.WindowCenter = (maximum + minimum) / 2
-#        ds.WindowWidth = maximum - minimum
+    array = np.transpose(array)
     ds.Rows = array.shape[0]
     ds.Columns = array.shape[1]
     ds.PixelData = array.tobytes()

dbdicom/utils/image.py

@@ -54,14 +54,13 @@ def dismantle_affine_matrix(affine):
     # ImagePositionPatient_i = ImagePositionPatient + i * SpacingBetweenSlices * slice_cosine
     column_spacing = np.linalg.norm(affine[:3, 0])
     row_spacing = np.linalg.norm(affine[:3, 1])
-    slice_thickness = np.linalg.norm(affine[:3, 2])
+    slice_spacing = np.linalg.norm(affine[:3, 2])
     row_cosine = affine[:3, 0] / column_spacing
     column_cosine = affine[:3, 1] / row_spacing
-    slice_cosine = affine[:3, 2] / slice_thickness
+    slice_cosine = affine[:3, 2] / slice_spacing
     return {
         'PixelSpacing': [row_spacing, column_spacing], 
-#        'SpacingBetweenSlices': slice_thickness,  # Obsolete
-        'SliceThickness': slice_thickness, 
+        'SpacingBetweenSlices': slice_spacing,  
         'ImageOrientationPatient': row_cosine.tolist() + column_cosine.tolist(), 
         'ImagePositionPatient': affine[:3, 3].tolist(), # first slice for a volume
         'slice_cosine': slice_cosine.tolist()} 

{dbdicom-0.3.2.dist-info → dbdicom-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dbdicom
-Version: 0.3.2
+Version: 0.3.4
 Summary: A pythonic interface for reading and writing DICOM databases
 Author-email: Steven Sourbron <s.sourbron@sheffield.ac.uk>, Ebony Gunwhy <e.gunwhy@sheffield.ac.uk>
 Project-URL: Homepage, https://openmiblab.github.io/dbdicom/

{dbdicom-0.3.2.dist-info → dbdicom-0.3.4.dist-info}/RECORD

@@ -1,21 +1,21 @@
 dbdicom/__init__.py,sha256=DyogeTraV6o-FgWdBCbtVEaMmdkMQHkYkraDIE0t8OA,25
-dbdicom/api.py,sha256=Xcur6TstwvSD8QMDkFn97NDnuVymjCtHWldimG8CDP4,9783
+dbdicom/api.py,sha256=gBBOgzg54zWA_Rf4392OyNBQUEHt3FYYTLq_QA75bUc,9596
 dbdicom/const.py,sha256=BqBiRRjeiSqDr1W6YvaayD8WKCjG4Cny2NT0GeLM6bI,4269
-dbdicom/database.py,sha256=w835qQHThZsIhoTXlQbZykcKnVrEADgp2mRYBTOKz4g,4627
-dbdicom/dataset.py,sha256=dm0bmBjqb_3uZLYV87gKszlqKMMLrSbaymVROafB5ac,22143
-dbdicom/dbd.py,sha256=xpDiWzlMUmXzYgRCR5jwvvHENbTsq3B89HvK2JxAo3c,26450
-dbdicom/register.py,sha256=5wBQsf4PB6ITHN3clUOMStUy5iYjMnIYUBfhVS2Drio,23692
+dbdicom/database.py,sha256=_LUbH7gc9l7j_63AC71DjwxgTUwbEjHSy5kuvRw75Hw,4764
+dbdicom/dataset.py,sha256=hLAyFlN7zQ-dOzI9V67aHfTq3VtpvCI7_83tnBqXObE,21880
+dbdicom/dbd.py,sha256=6ewuLQwiYGI5EtzWQskxk4CKoprc2gU-m-iSIMPNTv8,31090
+dbdicom/register.py,sha256=_NyNbOEAN_hkwjxupNpr9F5DWUwARCsci8knK41-EsA,13931
 dbdicom/external/__init__.py,sha256=XNQqfspyf6vFGedXlRKZsUB8k8E-0W19Uamwn8Aioxo,316
-dbdicom/external/__pycache__/__init__.cpython-311.pyc,sha256=cIySrImYKo1fJP3-0ZMV-5ZKcZEEDX-uwfZ7I4U-jRs,534
+dbdicom/external/__pycache__/__init__.cpython-311.pyc,sha256=pXAQ35ixd92fm6YcuHgzR1t6RcASQ-cHhU1wOA5b8sw,542
 dbdicom/external/dcm4che/README.md,sha256=0aAGRs36W3_0s5LzWHRGf_tqariS_JP4iJggaxnD4Xw,8987
 dbdicom/external/dcm4che/__init__.py,sha256=YwpeMCLrxffGOkchsGjgAuB6ia3VX_tx9Y7ru9EWtoY,35
-dbdicom/external/dcm4che/__pycache__/__init__.cpython-311.pyc,sha256=QsnVh0zH1ZSOoNwtTqiirWH8CB0b2eJ0DEvgVoVhZ0Y,248
+dbdicom/external/dcm4che/__pycache__/__init__.cpython-311.pyc,sha256=FB8wyWqXDUt_1P-QmE4yt9uD6dDm5YqYWjqVuRwGdSo,256
 dbdicom/external/dcm4che/bin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/bin/deidentify,sha256=64MNIEpp-CWzFSb6TV0KtyCBvD7XyEsovRjBeyxDqSc,1698
 dbdicom/external/dcm4che/bin/deidentify.bat,sha256=kVXUkcy1C4Y3KjC2NJwmmR0pufSJWmaof_LR5CTAxMg,1455
 dbdicom/external/dcm4che/bin/emf2sf,sha256=svCzkZ-QhdVTV0NNHOpBiwNBMODVWZHJIFA7cWaN2bM,1622
 dbdicom/external/dcm4che/bin/emf2sf.bat,sha256=Vh0ry9KNJX_WXcyCrLSxbJ_6Crot9rjmwi__u2GZqLY,1375
-dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-311.pyc,sha256=M2mla4vNW1gSUWQps3dx4g8NRd4BaQJLP1OKQHmi6Sk,195
+dbdicom/external/dcm4che/bin/__pycache__/__init__.cpython-311.pyc,sha256=GYcm47ETjYvRUN5RPTe5R-c0prd14GP8gm96eJcy0uQ,203
 dbdicom/external/dcm4che/etc/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/etc/emf2sf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dbdicom/external/dcm4che/etc/emf2sf/log4j.properties,sha256=3hHcBFt2oNRjvHtix5bfuEsnKfdv5IYOkbsyoY9g7cM,223
@@ -36,7 +36,7 @@ dbdicom/external/dcm4che/lib/windows-x86/opencv_java.dll,sha256=QanyzLy0Cd79-aOV
 dbdicom/external/dcm4che/lib/windows-x86-64/opencv_java.dll,sha256=TmjW2SbG4MR3GQ95T8xCVVDLgsdKukgaHBPUvWkfXp8,11039232
 dbdicom/sop_classes/ct_image.py,sha256=16PNv_0e1_7cfxE12JWlx5YQeaTAQVzwtXTjxs3aonk,2812
 dbdicom/sop_classes/enhanced_mr_image.py,sha256=13j4EGXniBpJxpzzL3Xa4y3g5OKhMd5Ct7cjPGOYQY4,35496
-dbdicom/sop_classes/mr_image.py,sha256=nHSQIh_zpdmZ0VhwKCVr9iqkluHxl1ASQ75Fr9OeNXI,10270
+dbdicom/sop_classes/mr_image.py,sha256=kNcrWXZ3VC3hhfqjMRjrlZOVqZH3Q5KfWXYLfLD-bEY,10913
 dbdicom/sop_classes/parametric_map.py,sha256=2OKBuC2bo03OEpKqimQS-nVGFp1cKRPYwVgmDGVf1JU,12288
 dbdicom/sop_classes/secondary_capture.py,sha256=wgNRX8qyhV7HR7Jq2tQWPPuGpiRzYl6qPOgK6qFbPUc,4541
 dbdicom/sop_classes/segmentation.py,sha256=I8-PciIoIz27_-dZ4esBZSw0TBBbO8KbNYTiTmVe62g,11465
@@ -45,10 +45,10 @@ dbdicom/sop_classes/xray_angiographic_image.py,sha256=nWysCGaEWKVNItnOgyJfcGMpS3
 dbdicom/utils/arrays.py,sha256=wiqCczLXlNl0qIePVOwCYvbAJhPveNorplkhtGleS48,1121
 dbdicom/utils/dcm4che.py,sha256=Vxq8NYWWK3BuqJkzhBQ89oMqzJlnxqTxgsgTo_Frznc,2317
 dbdicom/utils/files.py,sha256=qhWNJqeWnRjDNbERpC6Mz962_TW9mFdvd2lnBbK3xt4,2259
-dbdicom/utils/image.py,sha256=dCjukz9Zvpl4cP3KR1Y4hmKkox5KaFiEhdxDWDEdNec,4110
+dbdicom/utils/image.py,sha256=D46CD_ezpp2uq8VMqug5Z09fAyoJ9U6VwuxIFNJK8zg,4048
 dbdicom/utils/variables.py,sha256=vUh5cDnmCft5hoXDYXUvfkg5Cy5WlgMAogU38Y_BKRo,5753
-dbdicom-0.3.2.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
-dbdicom-0.3.2.dist-info/METADATA,sha256=zqs5ghuuW4o1UR_QkGhiM9afOqmKYWMg0d54ThWRV0k,1030
-dbdicom-0.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dbdicom-0.3.2.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
-dbdicom-0.3.2.dist-info/RECORD,,
+dbdicom-0.3.4.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+dbdicom-0.3.4.dist-info/METADATA,sha256=DPuzyZj81SfdTQGR_qogbbI1BxeG6StqSLM_pgnck44,1030
+dbdicom-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dbdicom-0.3.4.dist-info/top_level.txt,sha256=nJWxXg4YjD6QblfmhrzTMXcr8FSKNc0Yk-CAIDUsYkQ,8
+dbdicom-0.3.4.dist-info/RECORD,,