Branchless distance-driven BProj and Proj working

README.md

@@ -0,0 +1,71 @@
+pyDBT
+======
+
+This repository is a python extension of the [DBT toolbox](https://github.com/LAVI-USP/DBT-Reconstruction) from LAVI-USP. 
+
+
+
+## How to install?
+
+ 1. Download the toolbox or clone the directory:
+
+    * ```git clone https://github.com/LAVI-USP/pyDBT.git```
+
+ 2. Go to parent directory:
+
+    * ```cd pyDBT```
+
+ 3. Install the package:
+
+    * ```python3 setup.py install```
+
+ 4. run the example:
+
+    * ```cd pydbt && python3 example.py```
+
+ 5. The toolbox was tested on **Linux** (Ubuntu) x64, and **MacoS** Catalina machines, with python **3.7.5**.
+
+ 6. You can also run the [MATLAB version](https://github.com/LAVI-USP/DBT-Reconstruction) of the toolbox.
+
+** Please report issues [here](https://github.com/LAVI-USP/pyDBT/issues). **
+
+## Contribute? 
+
+We are pleased with any contributions. Fell free to make any [pull requests](https://github.com/LAVI-USP/pyDBT/pulls) or send us an e-mail.
+
+
+## Toolbox manual:
+
+You can find the [manual](https://github.com/LAVI-USP/DBT-Reconstruction/wiki/Toolbox-Manual) from the MATLAB version, which is pretty much the same. I will create a specific one for the python version in the future.
+
+## Contact:
+
+If you have any question or suggestion, please send us an e-mail:
+
+- Rodrigo - rodrigo dot vimieiro at gmail dot com
+- Marcelo - mvieira at sc dot usp dot br
+
+## License:
+
+The toolbox is licensed under the **GNU General Public License v3.0**. Please check the [licence file](https://github.com/LAVI-USP/pyDBT/blob/master/LICENSE).
+
+## Reference:
+
+If you use the toolbox, we will be very grateful if you refer to this [paper](https://doi.org/10.1007/978-981-13-2517-5_53):
+
+> Vimieiro R.B., Borges L.R., Vieira M.A.C. (2019) Open-Source Reconstruction Toolbox for Digital Breast Tomosynthesis. In: Costa-Felix R., Machado J., Alvarenga A. (eds) XXVI Brazilian Congress on Biomedical Engineering. IFMBE Proceedings, vol 70/2. Springer, Singapore.
+
+## Citations:
+
+You can find [here](https://scholar.google.com.br/scholar?oi=bibs&hl=pt-BR&cites=3156269064066227282) the papers that have used the toolbox.
+
+## Acknowledgments:
+
+This work was supported by the São Paulo Research Foundation ([FAPESP](http://www.fapesp.br/) grant 2016/25750-0) and by the National Council for Scientific and Technological Development ([CNPq](http://www.cnpq.br/)). Nobody does anything alone, so we would like to thank the contribution of our lab members and the [Barretos Love Hospital](https://www.hcancerbarretos.com.br) for providing the images of DBT.
+
+---
+
+Laboratory of Computer Vision ([Lavi](http://iris.sel.eesc.usp.br/lavi/))  
+Department of Electrical and Computer Engineering  
+São Carlos School of Engineering, University of São Paulo  
+São Carlos - Brazil

pydbt/example.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Jan 14 08:37:11 2020
+
+@author: Rodrigo
+"""
+
+#%%
+import matplotlib.pyplot as plt 
+
+from parameterSettings import geometry_settings
+from functions.manageDicom import readDicom
+from functions.dataPreProcess import dataPreProcess
+from functions.projectionDDb import projectionDDb
+from functions.backprojectionDDb import backprojectionDDb
+from functions.initialConfig import initialConfig
+
+#%% Call function for initial configurations
+
+libFiles = initialConfig()
+
+#%% Create a DBT geometry
+
+geo = geometry_settings()
+geo.GE()
+
+#%% Get DICOM data
+
+dcmPath = "/home/rodrigo/Downloads/imgs/"
+proj = readDicom(dcmPath,geo)
+
+proj = dataPreProcess(proj, geo)
+
+#%%
+
+print("Starting reconstruction...")
+
+vol = backprojectionDDb(proj, geo, libFiles)
+plt.figure()
+plt.title('Reconstructed slice')
+plt.imshow(vol[:,:,50] , cmap=plt.get_cmap('gist_gray'))
+
+print("Starting projection...")
+
+proj = projectionDDb(vol, geo, libFiles) 
+plt.figure()
+plt.title('Projected volume')
+plt.imshow(proj[:,:,4] , cmap=plt.get_cmap('gist_gray'))
+
+

pydbt/functions/backprojectionDDb.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jan 17 18:46:40 2020
+
+@author: Rodrigo
+"""
+
+import numpy as np
+import numpy.ctypeslib as ctl
+
+from functions.utilities import findAndLoadLibray
+from functions.utilities import geoAsNp
+
+def backprojectionDDb(proj, geo, libFiles):
+
+
+    # Check if the input is in proper size
+    if not (proj.shape[0] == geo.nv and proj.shape[1] == geo.nu and proj.shape[2] == geo.nProj):
+        raise ValueError('First argument needs to have the same number of rows, cols and slices as in the configuration file.')
+
+
+    # Find and library    
+    lib = findAndLoadLibray(libFiles, 'backprojectionDDb')
+
+
+    backprojectionDDb_lib = lib.backprojectionDDb_lib
+
+    backprojectionDDb_lib.argtypes = [ctl.ndpointer(np.float64, flags='aligned, c_contiguous'),
+                               ctl.ndpointer(np.float64, flags='aligned, c_contiguous'),
+                               ctl.ndpointer(np.float32, flags='aligned, c_contiguous')]
+
+
+    # Transform geo class in numpy array
+    geoNp = geoAsNp(geo) 
+
+
+    vol_transp = np.empty([geo.nz, geo.nx, geo.ny], dtype=np.float64)
+
+    proj_transp = np.transpose(proj, (2, 1, 0)).copy()
+
+    backprojectionDDb_lib (proj_transp, vol_transp, geoNp)
+
+    vol = np.transpose(vol_transp, (2, 1, 0)).copy()
+
+
+    return vol
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

pydbt/functions/dataPreProcess.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Oct 22 10:34:24 2019
+
+@author: rodrigo
+"""
+
+import numpy as np
+
+def dataPreProcess(proj, geo):
+
+    proj = cropProj(proj)
+
+    proj = transfIntensity(proj)
+
+    # Modifies parameters based on segmentation
+    geo.nu = proj.shape[1]  # Number of pixels (columns)
+
+    return proj
+
+
+
+def cropProj(proj):
+
+    Gap = 20;
+
+    maxValue = np.max(proj)
+
+    vertProj = np.sum(maxValue-proj[:,:,proj.shape[2]//2 - 1], axis=0)	# Horizontal Profile
+
+    Ind = np.argmax(np.diff(vertProj[10:])) - Gap   # Smooth the signal and takes its max positive derivative
+
+    proj_crop = proj[:,Ind:,:]
+
+    return proj_crop
+
+
+def transfIntensity(proj):
+
+     # Transform intensity image in attenuation coefficients
+    proj = -np.log(proj/np.max(proj)); 
+
+    return proj
+

pydbt/functions/initialConfig.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jan 22 13:35:00 2020
+
+@author: rodrigo
+"""
+
+import pathlib
+
+def initialConfig():
+
+    workDir = pathlib.Path().absolute()
+
+    outDir = workDir / 'output'
+
+    if not(outDir.exists() and outDir.is_dir()):
+        pathlib.Path(outDir).mkdir()
+
+    libFiles = findLibraries(workDir)
+
+    return libFiles
+
+
+def findLibraries(workDir):
+
+    buildDir = workDir / '../build' 
+
+    if not(buildDir.exists() and buildDir.is_dir()):
+        raise ValueError('Cannot find the build folder. Make sure to run the setup.py or follow the instructions on the package Github.')
+
+    libDir = []
+
+    # Find libray directory
+    for f in buildDir.iterdir():
+        if f.is_dir():
+            if 'lib.' in str(f):
+                libDir = f
+
+    # Test if libDir is empty
+    if not libDir:    
+        raise ValueError('Cannot find the lib folder. Make sure to run the setup.py or follow the instructions on the package Github.')
+
+    libFiles = []
+
+    # Find all .so files   
+    for libFile in pathlib.Path(libDir).glob('*.so'):
+        libFiles.append((str(libDir),str(libFile).split('/')[-1]))
+
+
+    return libFiles
+

pydbt/functions/manageDicom.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Oct  8 08:39:59 2019
+
+@author: rodrigo
+"""
+
+import pydicom
+import numpy as np
+from os import walk
+
+def readDicom(path, geo):
+
+    dcmFiles = []
+    for (_, _, filenames) in walk(path):
+        for file in filenames:
+            if file.endswith(".dcm"):
+                dcmFiles.append(file)
+        break
+
+    # Test if list is empty
+    if not dcmFiles:    
+        raise ValueError('No DICOM files found in the specified path.')
+
+    proj = np.zeros([geo.nv,geo.nu,geo.nProj],dtype='uint16')
+
+
+    for f in dcmFiles:
+        nProj = int(f.split('.')[0])
+        proj_dcmH = pydicom.dcmread(path + f)
+        proj[:,:,nProj]  = proj_dcmH.pixel_array
+
+    return proj

pydbt/functions/projectionDDb.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jan 17 13:36:50 2020
+
+@author: Rodrigo
+"""
+
+import numpy as np
+import numpy.ctypeslib as ctl
+
+from functions.utilities import findAndLoadLibray
+from functions.utilities import geoAsNp
+
+def projectionDDb(vol, geo, libFiles):
+
+
+    # Check if the input is in proper size
+    if not (vol.shape[0] == geo.ny and vol.shape[1] == geo.nx and vol.shape[2] == geo.nz):
+        raise ValueError('First argument needs to have the same number of rows, cols and slices as in the configuration file.')
+
+
+    # Find and library    
+    lib = findAndLoadLibray(libFiles, 'projectionDDb')
+
+
+    projectionDDb_lib = lib.projectionDDb_lib
+
+    projectionDDb_lib.argtypes = [ctl.ndpointer(np.float64, flags='aligned, c_contiguous'),
+                                  ctl.ndpointer(np.float64, flags='aligned, c_contiguous'),
+                                  ctl.ndpointer(np.float32, flags='aligned, c_contiguous')]
+
+
+    # Transform geo class in numpy array
+    geoNp = geoAsNp(geo)
+
+
+    proj_transp = np.empty([geo.nProj, geo.nu, geo.nv], dtype=np.float64)
+
+    vol_transp = np.transpose(vol, (2, 1, 0)).copy()
+
+    projectionDDb_lib (vol_transp, proj_transp, geoNp)
+
+    proj = np.transpose(proj_transp, (2, 1, 0)).copy()
+
+
+    return proj
+
+
+
+
+
+