Merge branch 'master' of https://github.com/vais-ral/CCPi-ReconstructionFramework

8 files changed, 65 insertions, 7 deletions

diff --git a/Wrappers/Python/ccpi/reconstruction/algs.py b/Wrappers/Python/ccpi/reconstruction/algs.py
index bfe9570..d957298 100644
--- a/Wrappers/Python/ccpi/reconstruction/algs.py
+++ b/Wrappers/Python/ccpi/reconstruction/algs.py
@@ -20,7 +20,7 @@
 import numpy
 import time
 
-from funcs import BaseFunction
+from ccpi.reconstruction.funcs import BaseFunction
 
 def FISTA(x_init, f=None, g=None, opt=None):
 
diff --git a/Wrappers/Python/ccpi/reconstruction/ops.py b/Wrappers/Python/ccpi/reconstruction/ops.py
index af8ead6..82f18ac 100644
--- a/Wrappers/Python/ccpi/reconstruction/ops.py
+++ b/Wrappers/Python/ccpi/reconstruction/ops.py
@@ -19,7 +19,7 @@
 
 import numpy
 from scipy.sparse.linalg import svds
-from framework import DataSet, VolumeData, SinogramData, DataSetProcessor
+from ccpi.framework import DataSet, VolumeData, SinogramData, DataSetProcessor
 
 # Maybe operators need to know what types they take as inputs/outputs
 # to not just use generic DataSet
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
index 0c6ad30..5dd97b0 100644
--- a/Wrappers/Python/conda-recipe/build.sh
+++ b/Wrappers/Python/conda-recipe/build.sh
@@ -5,5 +5,5 @@ fi
 mkdir ${SRC_DIR}/ccpi
 cp -r "${RECIPE_DIR}/../../../" ${SRC_DIR}/ccpi
 
-cd ${SRC_DIR}/ccpi/Wrappers/python
+cd ${SRC_DIR}/ccpi/Wrappers/Python
 $PYTHON setup.py install
diff --git a/Wrappers/Python/setup.py b/Wrappers/Python/setup.py
index 8ee6b58..bbd210f 100644
--- a/Wrappers/Python/setup.py
+++ b/Wrappers/Python/setup.py
@@ -35,7 +35,7 @@ if  cil_version == '':
 setup(
     name="ccpi-common",
     version=cil_version,
-    packages=['ccpi'],
+    packages=['ccpi' , 'ccpi.reconstruction'],
 
     # Project uses reStructuredText, so ensure that the docutils get
     # installed or upgraded on the target machine
diff --git a/Wrappers/Python/test/DemoRecIP.py b/Wrappers/Python/test/DemoRecIP.py
index 790e90e..483a202 100644
--- a/Wrappers/Python/test/DemoRecIP.py
+++ b/Wrappers/Python/test/DemoRecIP.py
@@ -8,13 +8,13 @@ import numpy as np
 import matplotlib.pyplot as plt
 
 import sys
-sys.path.append('../data/')
+#sys.path.append('../../../data/')
 from read_IPdata import read_IPdata
 
 from ccpi.reconstruction.astra_ops import AstraProjector
-from ccpi.reconstruction.funcs import Norm2sq
+from ccpi.reconstruction.funcs import Norm2sq , BaseFunction
 from ccpi.reconstruction.algs import FISTA
-from ccpi.reconstruction.ops import BaseFunction
+#from ccpi.reconstruction.funcs import BaseFunction
 
 from ccpi.framework import VolumeData, SinogramData
 
diff --git a/data/IP_data70channels.mat b/data/IP_data70channels.mat
new file mode 100644
index 0000000..19b9421
--- /dev/null
+++ b/data/IP_data70channels.mat
diff --git a/data/__pycache__/read_IPdata.cpython-35.pyc b/data/__pycache__/read_IPdata.cpython-35.pyc
new file mode 100644
index 0000000..b062cf9
--- /dev/null
+++ b/data/__pycache__/read_IPdata.cpython-35.pyc
diff --git a/data/read_IPdata.py b/data/read_IPdata.py
new file mode 100644
index 0000000..2e6a525
--- /dev/null
+++ b/data/read_IPdata.py
@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+function to read IP data and provide a dictionary with data and parameters as an output
+"""
+from scipy import io
+import numpy as np
+from collections import defaultdict
+
+def read_IPdata():
+    # read data from mat file (specify the location)
+    alldata = io.loadmat('IP_data70channels.mat')
+    data_raw = alldata.get('Data_raw') # here is raw projection data
+    Phantom_ideal = alldata.get('Phantom_ideal') # here is 70 channels ideal phantom
+    Photon_flux = alldata.get('Photon_flux') # photon flux for normalization
+    del alldata
+
+    # extract geometry-related parameters
+    proj_numb,detectors_numb,channels = np.shape(data_raw)
+    im_size  = np.size(Phantom_ideal,1)
+
+    theta = np.linspace(0,proj_numb-1,proj_numb)*360/proj_numb   # projection angles
+    dom_width   = 1.0       # width of domain in cm
+    src_to_rotc = 3.0       # dist. from source to rotation center
+    src_to_det  = 5.0       # dist. from source to detector
+    det_width   = 2.0       # detector width
+
+    # negative log normalisation of the raw data (avoiding of log(0))
+    data_norm = np.zeros(np.shape(data_raw))
+    for i in range(0,channels):
+        slice1 = data_raw[:,:,i]
+        indx = np.nonzero(slice1>0)
+        slice2 = np.zeros((proj_numb,detectors_numb), 'float32')
+        slice2[indx] = -np.log(slice1[indx]/Photon_flux[i])
+        indx2 = np.nonzero(slice1==0)
+        slice3 = np.zeros((proj_numb,detectors_numb), 'float32')
+        slice3[indx2] = np.log(slice2[indx2]+Photon_flux[i])
+        data_norm[:,:,i] = slice2 + slice3
+        del indx, indx2, slice1, slice2, slice3
+    data_norm = np.float32(data_norm*(im_size/dom_width))
+    
+    #build a dictionary for data and related parameters
+    dataDICT = defaultdict(list)
+    dataDICT['data_norm'].append(data_norm)
+    dataDICT['data_raw'].append(data_raw)
+    dataDICT['Photon_flux'].append(Photon_flux)
+    dataDICT['Phantom_ideal'].append(Phantom_ideal)
+    dataDICT['theta'].append(theta)
+    dataDICT['proj_numb'].append(proj_numb)
+    dataDICT['detectors_numb'].append(detectors_numb)
+    dataDICT['channels'].append(channels)
+    dataDICT['im_size'].append(im_size)
+    dataDICT['dom_width'].append(dom_width)
+    dataDICT['src_to_rotc'].append(src_to_rotc)
+    dataDICT['src_to_det'].append(src_to_det)
+    dataDICT['det_width'].append(det_width)
+    
+    return (dataDICT)
\ No newline at end of file