dbdicom 0.2.0__py3-none-any.whl → 0.2.3__py3-none-any.whl

dbdicom/utils/image.py

@@ -1,8 +1,94 @@
+import math
 import numpy as np
 from scipy.interpolate import interpn
 from scipy.ndimage import affine_transform
 
 
+def as_mosaic(array, rows=None):
+    """Reformat a 3D array (x,y,z) into a 2D mosaic"""
+
+    nz = array.shape[2]
+    if rows is None:
+        rows = math.ceil(math.sqrt(nz))
+    cols = math.ceil(nz/rows)
+    mosaic = np.zeros((array.shape[0]*cols, array.shape[1]*rows))
+    for k in range(nz):
+        j = math.floor(k/cols)
+        i = k-j*cols
+        mosaic[
+            i*array.shape[0]:(i+1)*array.shape[0],
+            j*array.shape[1]:(j+1)*array.shape[1],
+        ] = array[:,:,k]
+    return mosaic
+
+
+
+
+def ellipsoid(a, b, c, spacing=(1., 1., 1.), levelset=False):
+    """
+    Generates ellipsoid with semimajor axes aligned with grid dimensions
+    on grid with specified `spacing`.
+
+    Parameters
+    ----------
+    a : float
+        Length of semimajor axis aligned with x-axis.
+    b : float
+        Length of semimajor axis aligned with y-axis.
+    c : float
+        Length of semimajor axis aligned with z-axis.
+    spacing : tuple of floats, length 3
+        Spacing in (x, y, z) spatial dimensions.
+    levelset : bool
+        If True, returns the level set for this ellipsoid (signed level
+        set about zero, with positive denoting interior) as np.float64.
+        False returns a binarized version of said level set.
+
+    Returns
+    -------
+    ellip : (N, M, P) array
+        Ellipsoid centered in a correctly sized array for given `spacing`.
+        Boolean dtype unless `levelset=True`, in which case a float array is
+        returned with the level set above 0.0 representing the ellipsoid.
+
+    Note
+    ----
+    This function is copy-pasted directly from skimage source code without modification - this to avoid bringing in skimage as an essential dependency. 
+
+    """
+    if (a <= 0) or (b <= 0) or (c <= 0):
+        raise ValueError('Parameters a, b, and c must all be > 0')
+
+    offset = np.r_[1, 1, 1] * np.r_[spacing]
+
+    # Calculate limits, and ensure output volume is odd & symmetric
+    low = np.ceil(- np.r_[a, b, c] - offset)
+    high = np.floor(np.r_[a, b, c] + offset + 1)
+
+    for dim in range(3):
+        if (high[dim] - low[dim]) % 2 == 0:
+            low[dim] -= 1
+        num = np.arange(low[dim], high[dim], spacing[dim])
+        if 0 not in num:
+            low[dim] -= np.max(num[num < 0])
+
+    # Generate (anisotropic) spatial grid
+    x, y, z = np.mgrid[low[0]:high[0]:spacing[0],
+                       low[1]:high[1]:spacing[1],
+                       low[2]:high[2]:spacing[2]]
+
+    if not levelset:
+        arr = ((x / float(a)) ** 2 +
+               (y / float(b)) ** 2 +
+               (z / float(c)) ** 2) <= 1
+    else:
+        arr = ((x / float(a)) ** 2 +
+               (y / float(b)) ** 2 +
+               (z / float(c)) ** 2) - 1
+
+    return arr
+
+
 def multislice_affine_transform(array_source, affine_source, output_affine, slice_thickness=None, **kwargs):
     """Generalization of scipy's affine transform.
     
@@ -370,10 +456,10 @@ def affine_matrix(      # single slice function
     return affine 
 
 
-def slice_location(
-    image_orientation,  # ImageOrientationPatient
-    image_position,    # ImagePositionPatient
-    ):
+def slice_location( 
+    image_orientation:list,  # ImageOrientationPatient
+    image_position:list,    # ImagePositionPatient
+    ) -> float:
     """Calculate Slice Location"""
 
     row_cosine = np.array(image_orientation[:3])    
@@ -383,6 +469,27 @@ def slice_location(
     return np.dot(np.array(image_position), slice_cosine)
 
 
+def image_position_from_slice_location(slice_location:float, affine=np.eye(4))->list:
+    v = dismantle_affine_matrix(affine)
+    return list(affine[:3, 3] + slice_location * np.array(v['slice_cosine']))
+
+
+def image_position_patient(affine, number_of_slices):
+    slab = dismantle_affine_matrix(affine)
+    image_positions = []
+    image_locations = []
+    for s in range(number_of_slices):
+        pos = [
+            slab['ImagePositionPatient'][i] 
+            + s*slab['SpacingBetweenSlices']*slab['slice_cosine'][i]
+            for i in range(3)
+        ]
+        loc = np.dot(np.array(pos), np.array(slab['slice_cosine']))
+        image_positions.append(pos)
+        image_locations.append(loc)
+    return image_positions, image_locations
+
+
 def affine_matrix_multislice(
     image_orientation,  # ImageOrientationPatient (assume same for all slices)
     image_positions,    # ImagePositionPatient for all slices
@@ -442,22 +549,6 @@ def affine_to_RAH(affine):
     return np.matmul(rot_180, affine)
     
 
-def image_position_patient(affine, number_of_slices):
-    slab = dismantle_affine_matrix(affine)
-    image_positions = []
-    image_locations = []
-    for s in range(number_of_slices):
-        pos = [
-            slab['ImagePositionPatient'][i] 
-            + s*slab['SpacingBetweenSlices']*slab['slice_cosine'][i]
-            for i in range(3)
-        ]
-        loc = np.dot(np.array(pos), np.array(slab['slice_cosine']))
-        image_positions.append(pos)
-        image_locations.append(loc)
-    return image_positions, image_locations
-
-
 def clip(array, value_range = None):
 
     array[np.isnan(array)] = 0
@@ -467,7 +558,47 @@ def clip(array, value_range = None):
     return np.clip(array, value_range[0], value_range[1])
     
 
-def scale_to_range(array, bits_allocated):
+def scale_to_range(array, bits_allocated, signed=False):
+        
+    range = 2.0**bits_allocated - 1
+    if signed:
+        minval = -2.0**(bits_allocated-1)
+    else:
+        minval = 0
+    maximum = np.amax(array)
+    minimum = np.amin(array)
+    if maximum == minimum:
+        slope = 1
+    else:
+        slope = range / (maximum - minimum)
+    intercept = -slope * minimum + minval
+    array *= slope
+    array += intercept
+
+    if bits_allocated == 8:
+        if signed:
+            return array.astype(np.int8), slope, intercept
+        else:
+            return array.astype(np.uint8), slope, intercept
+    if bits_allocated == 16:
+        if signed:
+            return array.astype(np.int16), slope, intercept
+        else:
+            return array.astype(np.uint16), slope, intercept
+    if bits_allocated == 32:
+        if signed:
+            return array.astype(np.int32), slope, intercept
+        else:
+            return array.astype(np.uint32), slope, intercept
+    if bits_allocated == 64:
+        if signed:
+            return array.astype(np.int64), slope, intercept
+        else:
+            return array.astype(np.uint64), slope, intercept
+
+
+def _scale_to_range(array, bits_allocated):
+    # Obsolete - generalized as above
         
     range = 2.0**bits_allocated - 1
     maximum = np.amax(array)

dbdicom/utils/variables.py

@@ -20,8 +20,11 @@ def str_to_seconds(dicom_tm):
     return seconds_since_midnight
 
 def seconds_to_str(seconds_since_midnight):
-    if not isinstance(seconds_since_midnight, float): 
+    # if not isinstance(seconds_since_midnight, float): 
+    #     return None
+    if seconds_since_midnight is None:
         return None
+    seconds_since_midnight = float(seconds_since_midnight)
     hours = math.floor(seconds_since_midnight/3600)
     minutes = math.floor((seconds_since_midnight-hours*3600)/60)
     seconds = math.floor(seconds_since_midnight-hours*3600-minutes*60)
@@ -48,8 +51,11 @@ def time_to_seconds(tm):
     return seconds_since_midnight
 
 def seconds_to_time(seconds_since_midnight):
-    if not isinstance(seconds_since_midnight, float): 
+    # if not isinstance(seconds_since_midnight, float): 
+    #     return None
+    if seconds_since_midnight is None:
         return None
+    seconds_since_midnight = float(seconds_since_midnight)
     hours = math.floor(seconds_since_midnight/3600)
     minutes = math.floor((seconds_since_midnight-hours*3600)/60)
     seconds = math.floor(seconds_since_midnight-hours*3600-minutes*60)