Flat-field correction (without detector plane handling)

10 files changed, 473 insertions, 15 deletions

diff --git a/docs/todo.txt b/docs/todo.txt
index 88b518c..a9ab4c8 100644
--- a/docs/todo.txt
+++ b/docs/todo.txt
@@ -3,7 +3,9 @@ Main
  + Add plane/frame-number/broken metadata in the UFO buffers. Check propagation trough standard ufo filters. [ propogates trough processors, but not reductors ]
  + Plane selector filter
  - Handle packets with data from multiple datasets
- - Try UFO 'flat-field' correction filter
+ + Try UFO 'flat-field' correction filter [ works to a degree, but possible to make it better + anyway multiple planes will be needed later likely... ]
+ - Compute flat-/dark-fields per plane. 
+ - Support reading raw sinograms in get_reader (we need to set dimensions like in flat-/dark-fields, but howto handle parallel-sinograms/slices - function in config?)
  - Cone-beam to parallel-beam resampling ?
  - Full reconstruction chain
  - Try UFO visualization filter
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 116b400..bbbc5fb 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -5,6 +5,7 @@ set(ufofilter_SRCS
     ufo-roof-read-task.c
     ufo-roof-build-task.c
     ufo-roof-filter-task.c
+    ufo-roof-flat-field-correct.c
     )
 
 set(common_SRCS
diff --git a/src/kernels/meson.build b/src/kernels/meson.build
index 9803fb9..6472953 100644
--- a/src/kernels/meson.build
+++ b/src/kernels/meson.build
@@ -1,4 +1,5 @@
 kernel_files = [
+    'roof-ffc.cl'
 ]
 
 install_data(kernel_files,
diff --git a/src/kernels/roof-ffc.cl b/src/kernels/roof-ffc.cl
new file mode 100644
index 0000000..8752990
--- /dev/null
+++ b/src/kernels/roof-ffc.cl
@@ -0,0 +1,52 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+kernel void
+flat_correct (global float *corrected,
+              global float *data,
+              global const float *dark,
+              global const float *flat,
+              const int sinogram_input,
+              const int absorptivity,
+              const int fix_abnormal,
+              const float dark_scale,
+              const float flat_scale)
+{
+    const float eps = 1E-5;
+    const int gid = get_global_id(1) * get_global_size(0) + get_global_id(0);
+    const int corr_idx = sinogram_input ? get_global_id(0) : gid;
+    const float cdark = dark[corr_idx] * dark_scale;
+    const float cflat = flat[corr_idx] * flat_scale;
+    float result;
+
+    float nom = data[gid] - cdark;
+    float denom = cflat - cdark;
+
+    if (nom < eps) nom = eps;
+//    if (denom < eps) denom = eps;
+    if (denom < eps) denom = eps;
+    
+    result = -log(nom / denom);
+
+    if (fix_abnormal && (isnan (result) || isinf (result))) {
+        result = 0.0f;
+    }
+
+    corrected[gid] = result;
+}
diff --git a/src/meson.build b/src/meson.build
index 8f8930a..324c744 100644
--- a/src/meson.build
+++ b/src/meson.build
@@ -2,6 +2,7 @@ plugins = [
     'roof-read',
     'roof-build',
     'roof-filter',
+    'roof-flat-field-correct'
 ]
 
 roof_common_src = [
diff --git a/src/ufo-roof-flat-field-correct-task.c b/src/ufo-roof-flat-field-correct-task.c
new file mode 100644
index 0000000..7c1f9dc
--- /dev/null
+++ b/src/ufo-roof-flat-field-correct-task.c
@@ -0,0 +1,315 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifdef __APPLE__
+#include <OpenCL/cl.h>
+#else
+#include <CL/cl.h>
+#endif
+#include <math.h>
+#include "ufo-roof-flat-field-correct-task.h"
+
+
+struct _UfoRoofFlatFieldCorrectTaskPrivate {
+    gboolean fix_nan_and_inf;
+    gboolean absorptivity;
+    gboolean sinogram_input;
+    gfloat dark_scale;
+    gfloat flat_scale;
+    cl_kernel kernel;
+};
+
+static void ufo_task_interface_init (UfoTaskIface *iface);
+
+G_DEFINE_TYPE_WITH_CODE (UfoRoofFlatFieldCorrectTask, ufo_roof_flat_field_correct_task, UFO_TYPE_TASK_NODE,
+                         G_IMPLEMENT_INTERFACE (UFO_TYPE_TASK,
+                                                ufo_task_interface_init))
+
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE(obj) (G_TYPE_INSTANCE_GET_PRIVATE((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskPrivate))
+
+enum {
+    PROP_0,
+    PROP_FIX_NAN_AND_INF,
+    PROP_ABSORPTIVITY,
+    PROP_SINOGRAM_INPUT,
+    PROP_DARK_SCALE,
+    PROP_FLAT_SCALE,
+    N_PROPERTIES
+};
+
+static GParamSpec *properties[N_PROPERTIES] = { NULL, };
+
+UfoNode *
+ufo_roof_flat_field_correct_task_new (void)
+{
+    return UFO_NODE (g_object_new (UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, NULL));
+}
+
+static void
+ufo_roof_flat_field_correct_task_setup (UfoTask *task,
+                                   UfoResources *resources,
+                                   GError **error)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    priv->kernel = ufo_resources_get_kernel (resources, "roof-ffc.cl", "flat_correct", NULL, error);
+
+    if (priv->kernel)
+        UFO_RESOURCES_CHECK_SET_AND_RETURN (clRetainKernel (priv->kernel), error);
+}
+
+static void
+ufo_roof_flat_field_correct_task_get_requisition (UfoTask *task,
+                                             UfoBuffer **inputs,
+                                             UfoRequisition *requisition,
+                                             GError **error)
+{
+    ufo_buffer_get_requisition (inputs[0], requisition);
+
+    if (ufo_buffer_cmp_dimensions (inputs[1], requisition) != 0 ||
+        ufo_buffer_cmp_dimensions (inputs[2], requisition) != 0) {
+        g_set_error_literal (error, UFO_TASK_ERROR, UFO_TASK_ERROR_GET_REQUISITION,
+                             "flat-field-correct inputs must have the same size");
+    }
+}
+
+static guint
+ufo_roof_flat_field_correct_task_get_num_inputs (UfoTask *task)
+{
+    return 3;
+}
+
+static guint
+ufo_roof_flat_field_correct_task_get_num_dimensions (UfoTask *task, guint input)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    g_return_val_if_fail (input <= 2, 0);
+
+    /* A sinogram */
+    if (input == 0)
+        return 2;
+
+    /* A row of dark frame depend on the sinogram_input flag */
+    return priv->sinogram_input ? 1 : 2;
+}
+
+static UfoTaskMode
+ufo_roof_flat_field_correct_task_get_mode (UfoTask *task)
+{
+    return UFO_TASK_MODE_PROCESSOR | UFO_TASK_MODE_GPU;
+}
+
+static gboolean
+ufo_roof_flat_field_correct_task_process (UfoTask *task,
+                                        UfoBuffer **inputs,
+                                        UfoBuffer *output,
+                                        UfoRequisition *requisition)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+    UfoProfiler *profiler;
+    UfoGpuNode *node;
+
+    cl_command_queue cmd_queue;
+    cl_mem proj_mem;
+    cl_mem dark_mem;
+    cl_mem flat_mem;
+    cl_mem out_mem;
+    gint absorptivity, sino_in, fix_nan_and_inf;
+
+    node = UFO_GPU_NODE (ufo_task_node_get_proc_node (UFO_TASK_NODE (task)));
+    cmd_queue = ufo_gpu_node_get_cmd_queue (node);
+    proj_mem = ufo_buffer_get_device_array (inputs[0], cmd_queue);
+    dark_mem = ufo_buffer_get_device_array (inputs[1], cmd_queue);
+    flat_mem = ufo_buffer_get_device_array (inputs[2], cmd_queue);
+    out_mem = ufo_buffer_get_device_array (output, cmd_queue);
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (task);
+    absorptivity = (gint) priv->absorptivity;
+    sino_in = (gint) priv->sinogram_input;
+    fix_nan_and_inf = (gint) priv->fix_nan_and_inf;
+
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 0, sizeof (cl_mem), &out_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 1, sizeof (cl_mem), &proj_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 2, sizeof (cl_mem), &dark_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 3, sizeof (cl_mem), &flat_mem));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 4, sizeof (cl_int), &sino_in));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 5, sizeof (cl_int), &absorptivity));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 6, sizeof (cl_int), &fix_nan_and_inf));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 7, sizeof (cl_float), &priv->dark_scale));
+    UFO_RESOURCES_CHECK_CLERR (clSetKernelArg (priv->kernel, 8, sizeof (cl_float), &priv->flat_scale));
+
+    profiler = ufo_task_node_get_profiler (UFO_TASK_NODE (task));
+    ufo_profiler_call (profiler, cmd_queue, priv->kernel, 2, requisition->dims, NULL);
+
+    return TRUE;
+}
+
+static void
+ufo_roof_flat_field_correct_task_set_property (GObject *object,
+                                             guint property_id,
+                                             const GValue *value,
+                                             GParamSpec *pspec)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    switch (property_id) {
+        case PROP_FIX_NAN_AND_INF:
+            priv->fix_nan_and_inf = g_value_get_boolean (value);
+            break;
+        case PROP_ABSORPTIVITY:
+            priv->absorptivity = g_value_get_boolean (value);
+            break;
+        case PROP_SINOGRAM_INPUT:
+            priv->sinogram_input = g_value_get_boolean (value);
+            break;
+        case PROP_DARK_SCALE:
+            priv->dark_scale = g_value_get_float (value);
+            break;
+        case PROP_FLAT_SCALE:
+            priv->flat_scale = g_value_get_float (value);
+            break;
+
+        default:
+            G_OBJECT_WARN_INVALID_PROPERTY_ID (object, property_id, pspec);
+            break;
+    }
+}
+
+static void
+ufo_roof_flat_field_correct_task_get_property (GObject *object,
+                                             guint property_id,
+                                             GValue *value,
+                                             GParamSpec *pspec)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    switch (property_id) {
+        case PROP_FIX_NAN_AND_INF:
+            g_value_set_boolean (value, priv->fix_nan_and_inf);
+            break;
+        case PROP_ABSORPTIVITY:
+            g_value_set_boolean (value, priv->absorptivity);
+            break;
+        case PROP_SINOGRAM_INPUT:
+            g_value_set_boolean (value, priv->sinogram_input);
+            break;
+        case PROP_DARK_SCALE:
+            g_value_set_float (value, priv->dark_scale);
+            break;
+        case PROP_FLAT_SCALE:
+            g_value_set_float (value, priv->flat_scale);
+            break;
+        default:
+            G_OBJECT_WARN_INVALID_PROPERTY_ID (object, property_id, pspec);
+            break;
+    }
+}
+
+static void
+ufo_roof_flat_field_correct_task_finalize (GObject *object)
+{
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+
+    priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE (object);
+
+    if (priv->kernel) {
+        UFO_RESOURCES_CHECK_CLERR (clReleaseKernel (priv->kernel));
+        priv->kernel = NULL;
+    }
+
+    G_OBJECT_CLASS (ufo_roof_flat_field_correct_task_parent_class)->finalize (object);
+}
+
+static void
+ufo_task_interface_init (UfoTaskIface *iface)
+{
+    iface->setup = ufo_roof_flat_field_correct_task_setup;
+    iface->get_num_inputs = ufo_roof_flat_field_correct_task_get_num_inputs;
+    iface->get_num_dimensions = ufo_roof_flat_field_correct_task_get_num_dimensions;
+    iface->get_mode = ufo_roof_flat_field_correct_task_get_mode;
+    iface->get_requisition = ufo_roof_flat_field_correct_task_get_requisition;
+    iface->process = ufo_roof_flat_field_correct_task_process;
+}
+
+static void
+ufo_roof_flat_field_correct_task_class_init (UfoRoofFlatFieldCorrectTaskClass *klass)
+{
+    GObjectClass *gobject_class = G_OBJECT_CLASS (klass);
+
+    gobject_class->set_property = ufo_roof_flat_field_correct_task_set_property;
+    gobject_class->get_property = ufo_roof_flat_field_correct_task_get_property;
+    gobject_class->finalize = ufo_roof_flat_field_correct_task_finalize;
+
+    properties[PROP_FIX_NAN_AND_INF] =
+        g_param_spec_boolean("fix-nan-and-inf",
+            "Replace NAN and INF values with 0.0",
+            "Replace NAN and INF values with 0.0",
+            FALSE,
+            G_PARAM_READWRITE);
+
+/*
+    properties[PROP_ABSORPTIVITY] =
+        g_param_spec_boolean ("absorption-correct",
+            "Absorption correct",
+            "Absorption correct",
+            FALSE,
+            G_PARAM_READWRITE);
+
+    properties[PROP_SINOGRAM_INPUT] =
+        g_param_spec_boolean ("sinogram-input",
+            "If sinogram-input is True we correct only one line (the sinogram), thus darks are flats are 1D",
+            "If sinogram-input is True we correct only one line (the sinogram), thus darks are flats are 1D",
+            FALSE,
+            G_PARAM_READWRITE);
+*/
+
+    properties[PROP_DARK_SCALE] =
+        g_param_spec_float ("dark-scale",
+            "Scale the dark field prior to the flat field correct",
+            "Scale the dark field prior to the flat field correct",
+            -G_MAXFLOAT, G_MAXFLOAT, 1.0f,
+            G_PARAM_READWRITE);
+
+    properties[PROP_FLAT_SCALE] =
+        g_param_spec_float ("flat-scale",
+            "Scale the flat field prior to the flat field correct",
+            "Scale the flat field prior to the flat field correct",
+            -G_MAXFLOAT, G_MAXFLOAT, 1.0f,
+            G_PARAM_READWRITE);
+
+    for (guint i = PROP_0 + 1; i < N_PROPERTIES; i++)
+        g_object_class_install_property (gobject_class, i, properties[i]);
+
+    g_type_class_add_private (gobject_class, sizeof(UfoRoofFlatFieldCorrectTaskPrivate));
+}
+
+static void
+ufo_roof_flat_field_correct_task_init(UfoRoofFlatFieldCorrectTask *self)
+{
+    self->priv = UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_PRIVATE(self);
+    self->priv->fix_nan_and_inf = FALSE;
+    self->priv->absorptivity = FALSE;
+    self->priv->sinogram_input = FALSE;
+    self->priv->kernel = NULL;
+    self->priv->dark_scale = 1.0f;
+    self->priv->flat_scale = 1.0f;
+}
diff --git a/src/ufo-roof-flat-field-correct-task.h b/src/ufo-roof-flat-field-correct-task.h
new file mode 100644
index 0000000..ac82aaa
--- /dev/null
+++ b/src/ufo-roof-flat-field-correct-task.h
@@ -0,0 +1,67 @@
+/*
+ * Copyright (C) 2011-2013 Karlsruhe Institute of Technology
+ *
+ * This file is part of Ufo.
+ *
+ * This library is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation, either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef __UFO_ROOF_FLAT_FIELD_CORRECT_TASK_H
+#define __UFO_ROOF_FLAT_FIELD_CORRECT_TASK_H
+
+#include <ufo/ufo.h>
+
+G_BEGIN_DECLS
+
+#define UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK             (ufo_roof_flat_field_correct_task_get_type())
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK(obj)             (G_TYPE_CHECK_INSTANCE_CAST((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTask))
+#define UFO_IS_ROOF_FLAT_FIELD_CORRECT_TASK(obj)          (G_TYPE_CHECK_INSTANCE_TYPE((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK))
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_CLASS(klass)     (G_TYPE_CHECK_CLASS_CAST((klass), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskClass))
+#define UFO_IS_ROOF_FLAT_FIELD_CORRECT_TASK_CLASS(klass)  (G_TYPE_CHECK_CLASS_TYPE((klass), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK))
+#define UFO_ROOF_FLAT_FIELD_CORRECT_TASK_GET_CLASS(obj)   (G_TYPE_INSTANCE_GET_CLASS((obj), UFO_TYPE_ROOF_FLAT_FIELD_CORRECT_TASK, UfoRoofFlatFieldCorrectTaskClass))
+
+typedef struct _UfoRoofFlatFieldCorrectTask           UfoRoofFlatFieldCorrectTask;
+typedef struct _UfoRoofFlatFieldCorrectTaskClass      UfoRoofFlatFieldCorrectTaskClass;
+typedef struct _UfoRoofFlatFieldCorrectTaskPrivate    UfoRoofFlatFieldCorrectTaskPrivate;
+
+/**
+ * UfoRoofFlatFieldCorrectTask:
+ *
+ * [ADD DESCRIPTION HERE]. The contents of the #UfoRoofFlatFieldCorrectTask structure
+ * are private and should only be accessed via the provided API.
+ */
+struct _UfoRoofFlatFieldCorrectTask {
+    /*< private >*/
+    UfoTaskNode parent_instance;
+
+    UfoRoofFlatFieldCorrectTaskPrivate *priv;
+};
+
+/**
+ * UfoRoofFlatFieldCorrectTaskClass:
+ *
+ * #UfoRoofFlatFieldCorrectTask class
+ */
+struct _UfoRoofFlatFieldCorrectTaskClass {
+    /*< private >*/
+    UfoTaskNodeClass parent_class;
+};
+
+UfoNode  *ufo_roof_flat_field_correct_task_new       (void);
+GType     ufo_roof_flat_field_correct_task_get_type  (void);
+
+G_END_DECLS
+
+#endif
+
diff --git a/tests/roof/config.py b/tests/roof/config.py
index e085ed8..8f72014 100644
--- a/tests/roof/config.py
+++ b/tests/roof/config.py
@@ -13,10 +13,15 @@ class RoofConfig:
 
         self.path = self.get_opt('data', 'base_path', './')
         self.planes = self.get_opt('hardware', 'planes', 1)
-        self.modules = self.get_opt('hardware', 'modules', None)
-        self.streams = self.get_opt('network', 'streams', 1 if self.modules is None else self.modules)
+        self.modules = self.get_opt('hardware', 'modules', 0)
+        self.streams = self.get_opt('network', 'streams', self.modules if self.modules else 1)
         self.bit_depth = self.get_opt('hardware', 'bit_depth', 8)
 
+        self.sample_rate = self.get_opt('hardware', 'sample_rate', 0)
+        self.imaging_rate = self.get_opt('hardware', 'imaging_rate', 0)
+        self.fan_bins = self.modules * self.get_opt('hardware', 'channels_per_module', 16)
+        self.fan_projections = self.get_opt('hardware', 'samples_per_rotation', (self.sample_rate / self.imaging_rate) if (self.imaging_rate and self.sample_rate) else 1000)
+        
         if self.args.number is None: self.args.number = 0 if self.args.benchmark else self.planes
 
         # Consistency and default mode
@@ -46,6 +51,13 @@ class RoofConfig:
         if subpath is None: raise "Unknown data type %s is requested" % subpath
         return subpath if subpath.startswith('/') else  self.path + '/' + subpath
 
+    def get_roof_glob(self, data_type):
+        path = self.get_roof_path(data_type)
+        if path is None: return None
+
+        globre = re.compile('%.?(\d+)[luid]')
+        return globre.sub('*', path)
+
     def get_writer_type(self):
         return None if self.args.benchmark else self.args.write if self.args.write else 'raw_sinograms'
     
diff --git a/tests/roof/defaults.py b/tests/roof/defaults.py
index eed3fe5..f6b67f6 100644
--- a/tests/roof/defaults.py
+++ b/tests/roof/defaults.py
@@ -15,7 +15,7 @@ roof_default_paths = {
 #}
 
 roof_filters = {
- 'correction':                  [ "flat-field-correct" ],
+ 'correction':                  [ "roof-flat-field-correct" ],
  'reconstruction':              [ "roof-fan2par", "fft", "filter", "ifft", "backproject" ],
  'control':                     [ ],
  'visualization':               [ ]
@@ -23,9 +23,9 @@ roof_filters = {
 
 roof_data_types = {
  'correction': {
-    'flat_fields':              'flat-field-correct',
-    'dark_fields':              'flat-field-correct',
-    'raw_sinograms':            'flat-field-correct',
+    'flat_fields':              'roof-flat-field-correct',
+    'dark_fields':              'roof-flat-field-correct',
+    'raw_sinograms':            'roof-flat-field-correct',
     'fan_sinograms':            None    
   },
   'reconstruction': {
diff --git a/tests/roof/graph.py b/tests/roof/graph.py
index c34a3ed..495c629 100644
--- a/tests/roof/graph.py
+++ b/tests/roof/graph.py
@@ -39,11 +39,16 @@ class RoofGraph(RoofConfig):
         if (re.compile('roof').match(name)): kwargs.update(config = self.config_file)
         return self.save_task(stage, name, self.get_task(name, **kwargs))
     
+    def get_read_task(self, path):
+        params = { 'raw_width': self.fan_bins, 'raw_height': self.fan_projections, 'raw_bitdepth': self.bit_depth } if re.search('\.raw$', path) else { }
+        params['path'] = path
+        return self.get_task('read', **params)
+
     def get_reader(self):
         first = self.get_opt('data', 'first_file_number', 1)
         if self.args.read:
             # Reconstruction from standard UFO files
-            path = self.get_roof_path(self.args.read)
+            path = self.get_roof_glob(self.args.read)
             step = 1
             if (self.args.plane is not None) and (self.args.plane > 0): 
                 first += self.args.plane - 1;
@@ -54,6 +59,7 @@ class RoofGraph(RoofConfig):
                 params['number'] = self.args.number
             
             print ("Reading {} data from {}".format(self.args.read,path))
+            # FIXME: handle raw data parameters
             return self.get_task('read', **params)
         else:
             path = None
@@ -85,16 +91,16 @@ class RoofGraph(RoofConfig):
             write = self.get_task('write', filename=path)
         return write
 
-    def get_correction_flat_field_correct(self, head):
+    def get_correction_roof_flat_field_correct(self, head):
         # Standard UFO reconstruction stack distinguish flat/dark-fields recorded before and after experiment. We only do 'before experiment' part.
-        darks = self.get_roof_path('dark_fields')
+        darks = self.get_roof_glob('dark_fields')
         n_darks = len(get_filenames(darks))
         if n_darks == 0: raise FileNotFoundError("Dark fields are not found in {}".format(darks))
-        flats = self.get_roof_path('falt_fields')
+        flats = self.get_roof_glob('flat_fields')
         n_flats = len(get_filenames(flats))
         if n_flats == 0: raise FileNotFoundError("Flat fields are not found in {}".format(flats))
-        dark_reader = self.get_task('read', path = darks)
-        flat_reader = self.get_task('read', path = flats)
+        dark_reader = self.get_read_task(path = darks)
+        flat_reader = self.get_read_task(path = flats)
 
         # We are using standard get_task here because this is too generic plugin to allow config-based customization
         mode = self.get_opt('correction', 'aggregation', 'average')
@@ -116,7 +122,8 @@ class RoofGraph(RoofConfig):
         else:
             raise ValueError('Invalid reduction mode')
 
-        ffc = self.get_task('flat-field-correct') # dark_scale=args.dark_scale, absorption_correct=args.absorptivity, fix_nan_and_inf=args.fix_nan_and_inf)
+        #ffc = self.get_task('flat-field-correct', fix_nan_and_inf=False, absorption_correct=True)
+        ffc = self.get_task('roof-flat-field-correct', fix_nan_and_inf=False)  # absorption_correct=True)
         self.graph.connect_nodes_full(head, ffc, 0)
         self.graph.connect_nodes_full(dark_reduced, ffc, 1)
         self.graph.connect_nodes_full(flat_reduced, ffc, 2)
@@ -146,7 +153,7 @@ class RoofGraph(RoofConfig):
             if method in dir(self):
                 f = getattr(self, method)(head)
             else:
-                f = self.get_processor_task(stage, filters[pos])
+                f = self.get_processor_task(stage, filters[i])
                 graph.connect_nodes(head, f)
             head = f