From d528e08977568430f9e5da7ded54b5822d8256bc Mon Sep 17 00:00:00 2001
From: Thiago Franco de Moraes <totonixsame@gmail.com>
Date: Tue, 2 Jun 2020 17:23:54 -0300
Subject: [PATCH] Remove imgnormalize (FIX #235)

---
 invesalius/data/imagedata_utils.py       | 34 ++++------------------------------
 invesalius/segmentation/brain/segment.py |  2 +-
 2 files changed, 5 insertions(+), 31 deletions(-)

diff --git a/invesalius/data/imagedata_utils.py b/invesalius/data/imagedata_utils.py
index 8b9e362..e1fbd98 100644
--- a/invesalius/data/imagedata_utils.py
+++ b/invesalius/data/imagedata_utils.py
@@ -500,34 +500,6 @@ def img2memmap(group):
     return matrix, scalar_range, temp_file
 
 
-def imgnormalize(data, srange=(0, 255)):
-    """
-    Normalize image pixel intensity for int16 gray scale values.
-
-    :param data: image matrix
-    :param srange: range for normalization, default is 0 to 255
-    :return: normalized pixel intensity matrix
-    """
-
-    dataf = numpy.asarray(data)
-    rangef = numpy.asarray(srange)
-    faux = numpy.ravel(dataf).astype(float)
-    minimum = numpy.min(faux)
-    maximum = numpy.max(faux)
-    lower = rangef[0]
-    upper = rangef[1]
-
-    if minimum == maximum:
-        datan = numpy.ones(dataf.shape)*(upper + lower) / 2.
-    else:
-        datan = (faux-minimum)*(upper-lower) / (maximum-minimum) + lower
-
-    datan = numpy.reshape(datan, dataf.shape)
-    datan = datan.astype(numpy.int16)
-
-    return datan
-
-
 def get_LUT_value_255(data, window, level):
     shape = data.shape
     data_ = data.ravel()
@@ -539,6 +511,8 @@ def get_LUT_value_255(data, window, level):
     return data
 
 
-def image_normalize(image, min_=0.0, max_=1.0):
+def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):
+    output = np.empty(shape=image.shape, dtype=output_dtype)
     imin, imax = image.min(), image.max()
-    return (image - imin) * ((max_ - min_) / (imax - imin)) + min_
+    output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_
+    return output
diff --git a/invesalius/segmentation/brain/segment.py b/invesalius/segmentation/brain/segment.py
index 778d417..a79405a 100644
--- a/invesalius/segmentation/brain/segment.py
+++ b/invesalius/segmentation/brain/segment.py
@@ -64,7 +64,7 @@ def brain_segment(image, probability_array, comm_array):
     model.load_weights(str(folder.joinpath("model.h5")))
     model.compile("Adam", "binary_crossentropy")
 
-    image = imagedata_utils.image_normalize(image, 0.0, 1.0)
+    image = imagedata_utils.image_normalize(image, 0.0, 1.0, output_dtype=np.float32)
     sums = np.zeros_like(image)
     # segmenting by patches
     for completion, sub_image, patch in gen_patches(image, SIZE, OVERLAP):
--
libgit2 0.21.2