8 files changed, 585 insertions, 0 deletions
diff --git a/src/processors/FBP.py b/src/processors/FBP.py
new file mode 100644
index 0000000..c48c590
--- /dev/null
+++ b/src/processors/FBP.py
@@ -0,0 +1,32 @@
+from cil.framework import DataProcessor
+from cil.framework import DataOrder
+from src.processors.FBP_Standard import FBP_Standard
+from src.processors.FBP_Stacked import FBP_Stacked
+
+class FBP(DataProcessor):
+    def __init__(self, volume_geometry, sinogram_geometry, stacked=False, precision_mode='single', stack_num=2):
+        if stacked==True:
+            processor = FBP_Stacked(volume_geometry, sinogram_geometry, precision_mode, stack_num)
+        else:
+            processor = FBP_Standard(volume_geometry, sinogram_geometry)
+
+        super(FBP, self).__init__(volume_geometry=volume_geometry, sinogram_geometry=sinogram_geometry,
+                                  stacked=stacked,
+                                  precision_mode=precision_mode, stack_num=stack_num, processor=processor)
+
+        self.processor = processor
+
+    def set_input(self, dataset):
+        return self.processor.set_input(dataset)
+
+    def get_input(self):
+        return self.processor.get_input()
+
+    def get_output(self, out=None):
+        return self.processor.get_output(out=None)
+
+    def check_input(self, dataset):
+        return self.processor.check_input(dataset)
+
+    def process(self, out=None):
+        return self.processor.process(out=None)
diff --git a/src/processors/FBP_Stacked.py b/src/processors/FBP_Stacked.py
new file mode 100644
index 0000000..b6310a1
--- /dev/null
+++ b/src/processors/FBP_Stacked.py
@@ -0,0 +1,85 @@
+from cil.framework import DataProcessor, ImageData
+import numpy as np
+
+import gi
+gi.require_version('Ufo','0.0')
+from gi.repository import Ufo
+
+class FBP_Stacked(DataProcessor):
+    def __init__(self, volume_geometry,
+                 sinogram_geometry,
+                 precision_mode='single',
+                 stack_num=2):
+
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry,
+            'precision_mode': precision_mode,
+            'stack_num': stack_num}
+
+        super(FBP_Stacked, self).__init__(**kwargs)
+
+        self.precision_mode = precision_mode
+        self.stack_num = stack_num
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+        if self.sinogram_geometry.dimension == '2D':
+            raise ValueError("Expected input dimensions is 3, got {0}" \
+                             .format(dataset.number_of_dimensions))
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+        self.volume_geometry = volume_geometry
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+        self.sinogram_geometry = sinogram_geometry
+
+    def process(self, **kwargs):
+        # Get DATA
+        DATA = self.get_input()
+        DATA = DATA.as_array()
+
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = DATA.__array_interface__['data'][0]
+        read.props.width = DATA.shape[1]
+        read.props.height = DATA.shape[0]
+        read.props.number = DATA.shape[2]
+        read.props.bitdepth = 32
+
+        fft = pm.get_task('fft')
+        fft.props.dimensions = 1
+
+        filter = pm.get_task('filter')
+
+        ifft = pm.get_task('ifft')
+        ifft.props.dimensions = 1
+
+        stack = pm.get_task('stack')
+        stack.props.number = self.stack_num
+
+        stacked_bp = pm.get_task('stacked-backproject')
+        stacked_bp.props.axis_pos = DATA.shape[1] / 2
+        stacked_bp.props.precision_mode = self.precision_mode
+
+        vol_arr = np.zeros(self.volume_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = vol_arr.__array_interface__['data'][0]
+        write.props.max_size = vol_arr.nbytes
+
+        graph.connect_nodes(read, fft)
+        graph.connect_nodes(fft, filter)
+        graph.connect_nodes(filter, ifft)
+        graph.connect_nodes(ifft, stack)
+        graph.connect_nodes(stack, stacked_bp)
+        graph.connect_nodes(stacked_bp, write)
+
+        scheduler.run(graph)
+        vol_arr = ImageData(vol_arr, deep_copy=False, geometry=self.volume_geometry.copy(), suppress_warning=True)
+        return vol_arr
diff --git a/src/processors/FBP_Standard.py b/src/processors/FBP_Standard.py
new file mode 100644
index 0000000..3fdb91c
--- /dev/null
+++ b/src/processors/FBP_Standard.py
@@ -0,0 +1,80 @@
+from cil.framework import DataProcessor, ImageData
+import numpy as np
+
+import gi
+gi.require_version('Ufo','0.0')
+from gi.repository import Ufo
+
+class FBP_Standard(DataProcessor):
+    def __init__(self, volume_geometry,
+                 sinogram_geometry,
+                 z_dim = None):
+
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry,
+            'z_dim': z_dim}
+
+        super(FBP_Standard, self).__init__(**kwargs)
+
+        self.z_dim = 0
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+        if self.sinogram_geometry.dimension == '2D':
+            self.z_dim = 1
+        elif self.sinogram_geometry.dimension == '3D':
+            self.z_dim = self.sinogram_geometry.shape[2]
+
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+        self.volume_geometry = volume_geometry
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+        self.sinogram_geometry = sinogram_geometry
+
+    def process(self, **kwargs):
+        # Get DATA
+        DATA = self.get_input()
+        DATA = DATA.as_array()
+
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = DATA.__array_interface__['data'][0]
+        read.props.width = DATA.shape[1]
+        read.props.height = DATA.shape[0]
+        read.props.number = self.z_dim
+        read.props.bitdepth = 32
+
+        fft = pm.get_task('fft')
+        fft.props.dimensions = 1
+
+        filter = pm.get_task('filter')
+
+        ifft = pm.get_task('ifft')
+        ifft.props.dimensions = 1
+
+        bp = pm.get_task('backproject')
+        bp.props.axis_pos = DATA.shape[1] / 2
+
+        vol_arr = np.zeros(self.volume_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = vol_arr.__array_interface__['data'][0]
+        write.props.max_size = vol_arr.nbytes
+
+        graph.connect_nodes(read, fft)
+        graph.connect_nodes(fft, filter)
+        graph.connect_nodes(filter, ifft)
+        graph.connect_nodes(ifft, bp)
+        graph.connect_nodes(bp, write)
+
+        scheduler.run(graph)
+        vol_arr = ImageData(vol_arr, deep_copy=False, geometry=self.volume_geometry.copy(), suppress_warning=True)
+
+        return vol_arr
diff --git a/src/processors/UfoStackedBackProjector.py b/src/processors/UfoStackedBackProjector.py
new file mode 100644
index 0000000..a08b0c4
--- /dev/null
+++ b/src/processors/UfoStackedBackProjector.py
@@ -0,0 +1,101 @@
+import tifffile
+from cil.framework import DataProcessor, ImageData, DataOrder
+import gi
+
+gi.require_version('Ufo', '0.0')
+from gi.repository import Ufo
+import numpy as np
+
+
+class UfoStackedBackProjector(DataProcessor):
+
+    def __init__(self,
+                 volume_geometry=None,
+                 sinogram_geometry=None,
+                 precision_mode=None,
+                 stack_num=None):
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry,
+            'precision_mode': precision_mode,
+            'stack_num': stack_num}
+
+        super(UfoStackedBackProjector, self).__init__(**kwargs)
+
+        self.precision_mode = precision_mode
+        self.stack_num = stack_num
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+
+        if self.sinogram_geometry.shape != dataset.geometry.shape:
+            raise ValueError("Dataset not compatible with geometry used to create the projector")
+
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+
+        DataOrder.check_order_for_engine('astra', volume_geometry)
+
+        if len(volume_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(volume_geometry.number_of_dimensions))
+
+        self.volume_geometry = volume_geometry.copy()
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+
+        DataOrder.check_order_for_engine('astra', sinogram_geometry)
+
+        if len(sinogram_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(self.volume_geometry.number_of_dimensions))
+
+        self.sinogram_geometry = sinogram_geometry.copy()
+
+    def process(self, out=None):
+
+        DATA = self.get_input()
+
+        data_temp = DATA.as_array()
+
+        arr_out = self.create_backprojection(data_temp, out)
+
+        if out is None:
+            out = ImageData(arr_out, deep_copy=False, geometry=self.volume_geometry.copy(), suppress_warning=True)
+            return out
+        else:
+            out.fill(arr_out)
+
+    def create_backprojection(self, sino, vol):
+
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = sino.__array_interface__['data'][0]
+        read.props.width = sino.shape[0]
+        read.props.height = sino.shape[1]
+        read.props.number = sino.shape[2]
+        read.props.bitdepth = 32
+
+        stack = pm.get_task('stack')
+        stack.props.number = self.stack_num
+
+        stacked_bp = pm.get_task('stacked-backproject')
+        stacked_bp.props.axis_pos = sino.shape[1] / 2
+        stacked_bp.props.precision_mode = self.precision_mode
+
+        vol_arr = np.zeros(self.volume_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = vol_arr.__array_interface__['data'][0]
+        write.props.max_size = vol_arr.nbytes
+
+        graph.connect_nodes(read, stack)
+        graph.connect_nodes(stack, stacked_bp)
+        graph.connect_nodes(stacked_bp, write)
+
+        scheduler.run(graph)
+
+        return vol_arr
diff --git a/src/processors/UfoStackedForwardProjector.py b/src/processors/UfoStackedForwardProjector.py
new file mode 100644
index 0000000..86513c6
--- /dev/null
+++ b/src/processors/UfoStackedForwardProjector.py
@@ -0,0 +1,100 @@
+from cil.framework import DataProcessor, AcquisitionData, DataOrder
+
+import gi
+
+gi.require_version('Ufo', '0.0')
+from gi.repository import Ufo
+
+import numpy as np
+
+
+class UfoStackedForwardProjector(DataProcessor):
+    def __init__(self,
+                 volume_geometry=None,
+                 sinogram_geometry=None,
+                 precision_mode=None,
+                 stack_num=None):
+
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry,
+            'precision_mode': precision_mode,
+            'stack_num': stack_num
+        }
+
+        super(UfoStackedForwardProjector, self).__init__(**kwargs)
+
+        self.precision_mode = precision_mode
+        self.stack_num = stack_num
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+
+        if self.volume_geometry.shape != dataset.geometry.shape:
+            raise ValueError("Dataset not compatible with geometry used to create the projector")
+
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+
+        DataOrder.check_order_for_engine('astra', volume_geometry)
+
+        if len(volume_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(volume_geometry.number_of_dimensions))
+
+        self.volume_geometry = volume_geometry.copy()
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+
+        DataOrder.check_order_for_engine('astra', sinogram_geometry)
+
+        if len(sinogram_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(self.volume_geometry.number_of_dimensions))
+
+        self.sinogram_geometry = sinogram_geometry.copy()
+
+    def process(self, out=None):
+
+        IM = self.get_input()
+        data_temp = IM.as_array()
+
+        arr_out = self.create_sinogram(data_temp, out)
+
+        if out is None:
+            out = AcquisitionData(arr_out, deep_copy=False, geometry=self.sinogram_geometry.copy(),suppress_warning=True)
+            return out
+        else:
+            out.fill(arr_out)
+
+    def create_sinogram(self, vol, sino):
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = vol.__array_interface__['data'][0]
+        read.props.width = vol.shape[0]
+        read.props.height = vol.shape[1]
+        read.props.number = vol.shape[2]
+        read.props.bitdepth = 32
+
+        stack = pm.get_task('stack')
+        stack.props.number = self.stack_num
+
+        stacked_fp = pm.get_task('stacked-forwardproject')
+        stacked_fp.props.number = vol.shape[0]
+        stacked_fp.props.precision_mode = self.precision_mode
+
+        sino_arr = np.zeros(self.sinogram_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = sino_arr.__array_interface__['data'][0]
+        write.props.max_size = sino_arr.nbytes
+
+        graph.connect_nodes(read, stack)
+        graph.connect_nodes(stack, stacked_fp)
+        graph.connect_nodes(stacked_fp, write)
+
+        scheduler.run(graph)
+        return sino_arr
diff --git a/src/processors/UfoStandardBackProjector.py b/src/processors/UfoStandardBackProjector.py
new file mode 100644
index 0000000..ee27753
--- /dev/null
+++ b/src/processors/UfoStandardBackProjector.py
@@ -0,0 +1,93 @@
+#import tifffile
+from cil.framework import DataProcessor, ImageData, DataOrder
+import gi
+
+gi.require_version('Ufo', '0.0')
+from gi.repository import Ufo
+import numpy as np
+
+
+class UfoStandardBackProjector(DataProcessor):
+
+    def __init__(self,
+                 volume_geometry=None,
+                 sinogram_geometry=None):
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry}
+
+        super(UfoStandardBackProjector, self).__init__(**kwargs)
+
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+
+        if self.sinogram_geometry.shape != dataset.geometry.shape:
+            raise ValueError("Dataset not compatible with geometry used to create the projector")
+
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+
+        DataOrder.check_order_for_engine('astra', volume_geometry)
+
+        if len(volume_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(volume_geometry.number_of_dimensions))
+
+        self.volume_geometry = volume_geometry.copy()
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+
+        DataOrder.check_order_for_engine('astra', sinogram_geometry)
+
+        if len(sinogram_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(self.volume_geometry.number_of_dimensions))
+
+        self.sinogram_geometry = sinogram_geometry.copy()
+
+    def process(self, out=None):
+
+        DATA = self.get_input()
+
+        data_temp = DATA.as_array()
+
+        arr_out = self.create_backprojection(data_temp, out)
+
+        if out is None:
+            out = ImageData(arr_out, deep_copy=False, geometry=self.volume_geometry.copy(), suppress_warning=True)
+            return out
+        else:
+            out.fill(arr_out)
+
+    def create_backprojection(self, sino, vol):
+
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = sino.__array_interface__['data'][0]
+        read.props.width = sino.shape[1]
+        read.props.height = sino.shape[0]
+        if(len(sino.shape)==2):
+            read.props.number = 1
+        else:
+            read.props.number = sino.shape[2]
+        read.props.bitdepth = 32
+
+        backproject = pm.get_task('backproject')
+        backproject.props.axis_pos = sino.shape[1] / 2
+
+        vol_arr = np.zeros(self.volume_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = vol_arr.__array_interface__['data'][0]
+        write.props.max_size = vol_arr.nbytes
+
+        graph.connect_nodes(read, backproject)
+        graph.connect_nodes(backproject, write)
+
+        scheduler.run(graph)
+
+        return vol_arr
diff --git a/src/processors/UfoStandardForwardProjector.py b/src/processors/UfoStandardForwardProjector.py
new file mode 100644
index 0000000..bb6e0b4
--- /dev/null
+++ b/src/processors/UfoStandardForwardProjector.py
@@ -0,0 +1,89 @@
+from cil.framework import DataProcessor, AcquisitionData, DataOrder
+
+import gi
+gi.require_version('Ufo', '0.0')
+from gi.repository import Ufo
+
+import numpy as np
+
+class UfoStandardForwardProjector(DataProcessor):
+    def __init__(self,
+                 volume_geometry=None,
+                 sinogram_geometry=None):
+        kwargs = {
+            'volume_geometry': volume_geometry,
+            'sinogram_geometry': sinogram_geometry
+        }
+
+        super(UfoStandardForwardProjector, self).__init__(**kwargs)
+
+        self.set_ImageGeometry(volume_geometry)
+        self.set_AcquisitionGeometry(sinogram_geometry)
+
+    def check_input(self, dataset):
+
+        if self.volume_geometry.shape != dataset.geometry.shape:
+            raise ValueError("Dataset not compatible with geometry used to create the projector")
+
+        return True
+
+    def set_ImageGeometry(self, volume_geometry):
+
+        DataOrder.check_order_for_engine('astra', volume_geometry)
+
+        if len(volume_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(volume_geometry.number_of_dimensions))
+
+        self.volume_geometry = volume_geometry.copy()
+
+    def set_AcquisitionGeometry(self, sinogram_geometry):
+
+        DataOrder.check_order_for_engine('astra', sinogram_geometry)
+
+        if len(sinogram_geometry.dimension_labels) > 3:
+            raise ValueError("Supports 2D and 3D data only, got {0}".format(self.volume_geometry.number_of_dimensions))
+
+        self.sinogram_geometry = sinogram_geometry.copy()
+
+    def process(self, out=None):
+
+        IM = self.get_input()
+        data_temp = IM.as_array()
+
+        arr_out = self.create_sinogram(data_temp, out)
+
+        if out is None:
+            out = AcquisitionData(arr_out, deep_copy=False, geometry=self.sinogram_geometry.copy(),suppress_warning=True)
+            return out
+        else:
+            out.fill(arr_out)
+
+    def create_sinogram(self, vol, sino):
+        pm = Ufo.PluginManager()
+        graph = Ufo.TaskGraph()
+        scheduler = Ufo.Scheduler()
+
+        read = pm.get_task('memory-in')
+        read.props.pointer = vol.__array_interface__['data'][0]
+        read.props.width = vol.shape[1]
+        read.props.height = vol.shape[0]
+        if(len(vol.shape) == 2):
+            read.props.number = 1
+        else:
+            read.props.number = vol.shape[2]
+        read.props.bitdepth = 32
+
+        forwardproject = pm.get_task('forwardproject')
+        forwardproject.props.number = vol.shape[0]
+
+        sino_arr = np.zeros(self.sinogram_geometry.shape, dtype=np.float32)
+
+        write = pm.get_task('memory-out')
+        write.props.pointer = sino_arr.__array_interface__['data'][0]
+        write.props.max_size = sino_arr.nbytes
+
+        graph.connect_nodes(read, forwardproject)
+        graph.connect_nodes(forwardproject, write)
+
+        scheduler.run(graph)
+        return sino_arr
diff --git a/src/processors/__init__.py b/src/processors/__init__.py
new file mode 100644
index 0000000..c913057
--- /dev/null
+++ b/src/processors/__init__.py
@@ -0,0 +1,5 @@
+from .UfoStandardForwardProjector import UfoStandardForwardProjector
+from .UfoStandardBackProjector import UfoStandardBackProjector
+from .UfoStackedForwardProjector import UfoStackedForwardProjector
+from .UfoStackedBackProjector import UfoStackedBackProjector
+from .FBP import FBP