dicube 0.1.4__cp312-cp312-macosx_11_0_arm64.whl → 0.2.2__cp312-cp312-macosx_11_0_arm64.whl

dicube/storage/pixel_utils.py

@@ -31,37 +31,37 @@ def derive_pixel_header_from_array(
     dtype = str(image.dtype)
     if image.dtype in (np.uint16, np.uint8, np.uint32):
         return image, PixelDataHeader(
-            RESCALE_SLOPE=1,
-            RESCALE_INTERCEPT=0,
-            PIXEL_DTYPE=dtype,
-            ORIGINAL_PIXEL_DTYPE=dtype,
+            RescaleSlope=1,
+            RescaleIntercept=0,
+            PixelDtype=dtype,
+            OriginalPixelDtype=dtype,
         )
     elif image.dtype == np.int16:
         min_val = int(np.min(image))
         image = (image - min_val).astype("uint16")
         return image, PixelDataHeader(
-            RESCALE_SLOPE=1,
-            RESCALE_INTERCEPT=min_val,
-            PIXEL_DTYPE="uint16",
-            ORIGINAL_PIXEL_DTYPE=dtype,
+            RescaleSlope=1,
+            RescaleIntercept=min_val,
+            PixelDtype="uint16",
+            OriginalPixelDtype=dtype,
         )
     elif image.dtype == np.int8:
         min_val = int(np.min(image))
         image = (image - min_val).astype("uint8")
         return image, PixelDataHeader(
-            RESCALE_SLOPE=1,
-            RESCALE_INTERCEPT=min_val,
-            PIXEL_DTYPE="uint8",
-            ORIGINAL_PIXEL_DTYPE=dtype,
+            RescaleSlope=1,
+            RescaleIntercept=min_val,
+            PixelDtype="uint8",
+            OriginalPixelDtype=dtype,
         )
     elif image.dtype == np.int32:
         min_val = int(np.min(image))
         image = (image - min_val).astype("uint32")
         return image, PixelDataHeader(
-            RESCALE_SLOPE=1,
-            RESCALE_INTERCEPT=min_val,
-            PIXEL_DTYPE="uint32",
-            ORIGINAL_PIXEL_DTYPE=dtype,
+            RescaleSlope=1,
+            RescaleIntercept=min_val,
+            PixelDtype="uint32",
+            OriginalPixelDtype=dtype,
         )
     elif image.dtype in (np.float16, np.float32, np.float64):
         if preferred_dtype == "uint8":
@@ -78,10 +78,10 @@ def derive_pixel_header_from_array(
             # Set all pixels to 0, slope=0, intercept=min_val
             # When reading back: i*slope+intercept = min_val
             header = PixelDataHeader(
-                RESCALE_SLOPE=1.0,
-                RESCALE_INTERCEPT=float(min_val),
-                PIXEL_DTYPE=preferred_dtype,
-                ORIGINAL_PIXEL_DTYPE=dtype,
+                RescaleSlope=1.0,
+                RescaleIntercept=float(min_val),
+                PixelDtype=preferred_dtype,
+                OriginalPixelDtype=dtype,
             )
             raw_image = np.zeros_like(image, dtype=preferred_dtype)
             return raw_image, header
@@ -92,12 +92,12 @@ def derive_pixel_header_from_array(
                 preferred_dtype
             )
             header = PixelDataHeader(
-                RESCALE_SLOPE=slope,
-                RESCALE_INTERCEPT=intercept,
-                PIXEL_DTYPE=preferred_dtype,
-                ORIGINAL_PIXEL_DTYPE=dtype,
-                MAX_VAL=max_val,
-                MIN_VAL=min_val,
+                RescaleSlope=slope,
+                RescaleIntercept=intercept,
+                PixelDtype=preferred_dtype,
+                OriginalPixelDtype=dtype,
+                MaxVal=max_val,
+                MinVal=min_val,
             )
             return raw_image, header
     else:
@@ -132,10 +132,128 @@ def get_float_data(
 
     # Note: Output may be positive or negative depending on original dtype and slope/intercept
     output_img = raw_image.astype(dtype)
-    if pixel_header.RESCALE_SLOPE is not None:
-        slope = np.array(pixel_header.RESCALE_SLOPE).astype(dtype)
-        output_img *= slope
-    if pixel_header.RESCALE_INTERCEPT is not None:
-        intercept = np.array(pixel_header.RESCALE_INTERCEPT).astype(dtype)
-        output_img += intercept
-    return output_img 
+    if pixel_header.RescaleSlope is not None:
+        slope = np.array(pixel_header.RescaleSlope).astype(dtype)
+        if slope != 1.0:
+            output_img *= slope
+    if pixel_header.RescaleIntercept is not None:
+        intercept = np.array(pixel_header.RescaleIntercept).astype(dtype)
+        if intercept != 0.0:
+            output_img += intercept
+    return output_img
+
+
+def determine_optimal_nifti_dtype(
+    image: np.ndarray, pixel_header: PixelDataHeader
+) -> Tuple[np.ndarray, str]:
+    """Determine the optimal data type for saving to NIfTI and return the converted data.
+
+    This function selects the most appropriate data type for NIfTI export based on the value range
+    of the raw image and the rescale slope/intercept. It minimizes unnecessary data conversion and
+    only applies scaling or offset if needed.
+
+    Args:
+        image (np.ndarray): The raw image data (integer type guaranteed).
+        pixel_header (PixelDataHeader): Pixel header containing rescale information.
+
+    Returns:
+        Tuple[np.ndarray, str]:
+            - The image data converted to the optimal type for NIfTI export.
+            - The name of the chosen data type as a string.
+
+    Raises:
+        ValueError: If the data cannot be represented in any supported NIfTI type.
+
+    Example:
+        >>> arr = np.array([0, 100, 200], dtype=np.uint16)
+        >>> header = PixelDataHeader(RescaleSlope=1.0, RescaleIntercept=0.0, OriginalPixelDtype="uint16", PixelDtype="uint16")
+        >>> data, dtype_name = determine_optimal_nifti_dtype(arr, header)
+        >>> print(data.dtype, dtype_name)
+        uint8 uint8
+    """
+    # 获取slope和intercept
+    slope = pixel_header.RescaleSlope if pixel_header.RescaleSlope is not None else 1.0
+    intercept = pixel_header.RescaleIntercept if pixel_header.RescaleIntercept is not None else 0.0
+    
+    # 直接从原始数据计算值域
+    raw_min = float(image.min())
+    raw_max = float(image.max())
+    
+    # 计算应用slope和intercept后的值域
+    min_val = raw_min * slope + intercept
+    max_val = raw_max * slope + intercept
+    
+    # 如果斜率为负，需要交换min和max
+    if slope < 0:
+        min_val, max_val = max_val, min_val
+    
+    # 检查原始数据类型
+    original_dtype = pixel_header.OriginalPixelDtype
+    is_signed_original = original_dtype in ("int8", "int16", "int32", "int64")
+    
+    # 检查slope和intercept是否为整数值
+    has_integer_transform = (
+        np.isclose(slope % 1, 0) and 
+        np.isclose(intercept % 1, 0)
+    )
+    
+    # 准备最终数据 - 仅在确定dtype后执行一次转换
+    result_dtype = None
+    result_dtype_name = None
+    
+    # 如果slope和intercept都是整数，则可以使用整数类型
+    if has_integer_transform:
+        # 尊重原始数据类型的符号属性
+        if is_signed_original or min_val < 0:
+            # 有符号整数
+            if min_val >= -128 and max_val <= 127:
+                result_dtype = np.int8
+                result_dtype_name = "int8"
+            elif min_val >= -32768 and max_val <= 32767:
+                result_dtype = np.int16
+                result_dtype_name = "int16"
+            elif min_val >= -2147483648 and max_val <= 2147483647:
+                result_dtype = np.int32
+                result_dtype_name = "int32"
+            elif max_val <= 2147483647:  # 值域在int32范围内，但原始类型是int32
+                result_dtype = np.int32
+                result_dtype_name = "int32"
+        else:
+            # 无符号整数
+            if max_val <= 255:
+                result_dtype = np.uint8
+                result_dtype_name = "uint8"
+            elif max_val <= 65535:
+                result_dtype = np.uint16
+                result_dtype_name = "uint16"
+            elif max_val <= 4294967295:
+                result_dtype = np.uint32
+                result_dtype_name = "uint32"
+    
+    # 如果没有找到合适的整数类型，使用浮点类型
+    if result_dtype is None:
+        if np.issubdtype(image.dtype, np.float64) or min_val < -3.4e38 or max_val > 3.4e38:
+            result_dtype = np.float64
+            result_dtype_name = "float64"
+        else:
+            result_dtype = np.float32
+            result_dtype_name = "float32"
+            
+    if has_integer_transform:
+        intercept = int(intercept)
+    else:
+        intercept = np.array(intercept,dtype=result_dtype)
+
+    if slope == 1.0:
+        # 只要加法
+        return image.astype(result_dtype) + intercept, result_dtype_name
+    else:
+        # 需要乘法，生成最终数据
+        if result_dtype in (np.float32, np.float64):
+            # 浮点类型，直接使用浮点运算
+            result = image.astype(result_dtype) * slope + intercept
+        else:
+            # 整数类型，先做浮点运算再转换
+            result = (image.astype(np.float32) * slope + intercept).astype(result_dtype)
+        
+        return result, result_dtype_name 

{dicube-0.1.4.dist-info → dicube-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dicube
-Version: 0.1.4
+Version: 0.2.2
 Summary: Medical Image Storage Library with DICOM compatibility
 Author: Fangzhou Liao
 License: MIT
@@ -38,6 +38,7 @@ Requires-Dist: mypy>=1.0.0; extra == "dev"
 Requires-Dist: build>=0.8.0; extra == "dev"
 Requires-Dist: pylibjpeg>=2.0; extra == "dev"
 Requires-Dist: pylibjpeg-openjpeg>=2.0; extra == "dev"
+Requires-Dist: nibabel>=3.2.0; extra == "dev"
 Provides-Extra: all
 Requires-Dist: pybind11>=2.10.0; extra == "all"
 Requires-Dist: nibabel>=3.2.0; extra == "all"

{dicube-0.1.4.dist-info → dicube-0.2.2.dist-info}/RECORD

@@ -1,4 +1,7 @@
-dicube/__init__.py,sha256=QRyaQXqrzwSo8utXhGsbToE_lCEsjlzdzwFwVHINS8I,4189
+dicube-0.2.2.dist-info/RECORD,,
+dicube-0.2.2.dist-info/WHEEL,sha256=v7i1yNVEHWKlHHcCQ8SYkgpldhmAvPDAYWfI_XMFumo,114
+dicube-0.2.2.dist-info/METADATA,sha256=nBhXpfkqIUhGO2LUB-HmTwmDIolxcvd-cr8tW4CJNzM,10627
+dicube/__init__.py,sha256=TK2-JGOB_aPa6ilHw4WUc9l5Whc3Fb-tlZSPzbf5HIw,4886
 dicube/exceptions.py,sha256=YrwBD93oWI4yhvFfO-SOPCNMQ4z_1FSVL2gCVSnx-LU,6689
 dicube/validation.py,sha256=Edmx3yKhRShdzvM7uRK6N9j58GNV8rUv_k9w43JcaMs,12478
 dicube/codecs/__init__.py,sha256=NNus-iAv4JXsNH1kALf5vnLYnESFBoYaN72yJ7kQoqk,3754
@@ -14,22 +17,19 @@ dicube/codecs/jph/ojph_complete.cpython-311-darwin.so,sha256=SmXvkyjn1iCLHfLcmav
 dicube/codecs/jph/ojph_decode_complete.cpython-311-darwin.so,sha256=1aXbLZWb6nDX4e2S73dcWW8BnMUytk5AtWIzyxt4aiM,449096
 dicube/codecs/jph/ojph_decode_complete.cpython-39-darwin.so,sha256=OMAfYyAQra6xF_Zv5Y-LGBkg68MYpTK4qwB8lWqlf6U,448968
 dicube/codecs/jph/codec.py,sha256=d4bAoVAatSrWiC1k7gQLzWODZZTGo_1xeRRXO0NAtqo,5460
-dicube/core/io.py,sha256=9Wg9dmVCnZpXQH5fKiS152sKDyy4vOO7ChYpgRL-vzE,13763
+dicube/core/io.py,sha256=g8uKbcX7zz9LCq65spBeeodZEf6l4HSF9jzl60HZVyw,15629
 dicube/core/__init__.py,sha256=tU9vaPHbTkF8V78T8D6werr0nC7k6bMPIlatEIEdHU4,656
-dicube/core/pixel_header.py,sha256=M-zu5hFG0BWj0chWgxyGFAQP7oH7r-1iN44acKOLm7k,3929
-dicube/core/image.py,sha256=5XafyshOQbife6M8_G3vmrensjc1jTjyeUkAfAOCKiI,14182
+dicube/core/pixel_header.py,sha256=x3-gNiyL4lFRQ6c1TVdvsm2mG36xCQx78hq4vjYkqJI,4005
+dicube/core/image.py,sha256=DAyBwKlWeCU6oDWsmdSdAzVW3IieHNLUINIAhS_ZtRg,14177
 dicube/utils/__init__.py,sha256=m3pYJfuk4hISVes_cfG2eDjTyGF-y40xbxV07IOjbi0,149
 dicube/storage/__init__.py,sha256=q36sJqdI9acURBXjOW_g3QiyHw0XLGFCukMsQ-qioZc,465
-dicube/storage/dcb_file.py,sha256=Gsb_LXHAm7DqAdrh4Kgo0rrj1mUuz7sY6tVt8HiKXyI,30379
-dicube/storage/pixel_utils.py,sha256=thyYO-YNtWEvg1ROPLC-zPWqa37O0vJ8e26h3aF6dXM,5136
-dicube/dicom/dcb_streaming.py,sha256=6HUmk5QEdg8WhkaiiUDjdX8yMwQxABjmaXaDjxwQuQU,9042
+dicube/storage/dcb_file.py,sha256=GfOx2C6fexKojxwzak3_Q0K3gRBHB_UTMNVBY4NPRzg,31232
+dicube/storage/pixel_utils.py,sha256=-xMMnjSMzYk6WRvLAPktMELhSXJPmLBnt5wxKgOw5zg,9759
+dicube/dicom/dcb_streaming.py,sha256=Acsdusc6jIKuu1kd-VuDOoteZGdpt3UmwsxF-HQYZtM,9088
 dicube/dicom/dicom_meta.py,sha256=Iv-kEcV39vhK2qgSqGpqDhgg28RuUm8ddzSdpToIVPc,26813
-dicube/dicom/dicom_io.py,sha256=P-arcQu-CUB0Uf5daLku_Wf-3D3NpY3PiWHaosoe3dA,4941
+dicube/dicom/dicom_io.py,sha256=EBa72RGHfifFKygBwCWf6r2YCTNxE9onO8d65ws_5VU,4917
 dicube/dicom/dicom_status.py,sha256=NXi-sj3mhyaFGfpechewTjhI201vziVsyfLotsLr3Fs,10117
 dicube/dicom/__init__.py,sha256=9b7liSXx5vlpEYAr59GZGkcUw16kULELTX5SlLfcXPw,371
 dicube/dicom/merge_utils.py,sha256=6flzoK_6gzpvv4WSTaWq4SjVdr1gh3gtUPMsRfKDSNM,9312
 dicube/dicom/space_from_meta.py,sha256=__B7UTmvgV1N-LMJg9O_ObHgNWa39mbRF4ZSkQXm3Vs,2420
 dicube/dicom/dicom_tags.py,sha256=sOjrK9SoAhGqynF0e3YH70j8wbtvwGRezV-tM0wp40Q,3945
-dicube-0.1.4.dist-info/RECORD,,
-dicube-0.1.4.dist-info/WHEEL,sha256=v7i1yNVEHWKlHHcCQ8SYkgpldhmAvPDAYWfI_XMFumo,114
-dicube-0.1.4.dist-info/METADATA,sha256=lLPPqXaJcIOIHhGuU3buJPhmi3GCMeKi5KW0FhlY0nk,10581