nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/nabu_config.py

@@ -0,0 +1,175 @@
+from ..fullfield.nabu_config import *
+import copy
+
+## keep the text below for future inclusion in the documentation
+# start_z, end_z , start_z_mm, end_z_mm
+# ----------------------------------------------------------------
+# By default, all the volume is reconstructed slice by slice, along the axis 'z'.
+# ** option 1) you can set
+#     start_z_mm=0
+#     end_z_mm  = 0
+#
+#     Now, concerning start_z and end_z,  Use positive integers, with start_z < end_z
+#               The reconstructed vertical region will be
+#                   slice start = first doable + start_z
+#                   slice end   = first doable + end_z
+#                or less if such range needs to be clipped to the doable one
+#
+#                As an example start_z= 10, end_z = 20
+#                for reconstructing 10 slices close to scan start.
+#                NOTE: we are proceeding in the direction of the scan so that, in millimiters,
+#                       the start may be above or below the end
+#      To reconstruct the whole doable volume set
+#
+#        start_z= 0
+#        end_z  =-1
+#
+# ** option 2) using start_z_mm, end_z_mm
+#               Use positive floats, in millimiters. They indicate the height above the sample stage
+#             The values of start_z and end_z are not used in this case
+
+
+help_start_end_z = """ If  start_z_mm , end_z_mm are seto to zero, then start_z and end_z will be effective unless  end_z_fract  is different from zero. In this latter case the vertical range will be given in terms o the fractional position between the first doable and last doable slices.
+Otherwhise, if start_z_mm and end_z_mm are not zero,  the slices whose height above the sample stage, in millimiters, between start_z_mm and end_z_mm are reconstructed
+"""
+
+# we need to deepcopy this in order not to mess the original nabu_config of the full-field pipeline
+nabu_config = copy.deepcopy(nabu_config)
+
+nabu_config["preproc"]["processes_file"] = {
+    "default": "",
+    "help": "Path tgo the file where some operations should be stored for later use. By default it is 'xxx_nabu_processes.h5'",
+    "validator": optional_file_location_validator,
+    "type": "required",
+}
+nabu_config["preproc"]["double_flatfield_enabled"]["default"] = 1
+
+
+nabu_config["reconstruction"].update(
+    {
+        "dz_per_proj": {
+            "default": 0,
+            "help": " A positive DZPERPROJ means that the rotation axis is going up. Alternatively the vertical translations, can be given through an array using the variable z_per_proj_file",
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "z_per_proj_file": {
+            "default": "",
+            "help": "Alternative to dz_per_proj. A file where each line has one value: vertical displacements of the axis. There should be as many values as there are projection images.",
+            "validator": optional_file_location_validator,
+            "type": "optional",
+        },
+        "dx_per_proj": {
+            "default": 0,
+            "help": " A positive value means that the rotation axis is going on the rigth. Alternatively the horizontal translations, can be given through an array using the variable x_per_proj_file",
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "x_per_proj_file": {
+            "default": "",
+            "help": "Alternative to dx_per_proj. A file where each line has one value: horizontal displacements of the axis. There should be as many values as there are projection images.",
+            "validator": optional_file_location_validator,
+            "type": "optional",
+        },
+        "axis_to_the_center": {
+            "default": "1",
+            "help": "Whether to shift start_x and start_y so to have the axis at the center",
+            "validator": boolean_validator,
+            "type": "optional",
+        },
+        "auto_size": {
+            "default": "1",
+            "help": "Wether to set automatically start_x end_x start_y end_y ",
+            "validator": boolean_validator,
+            "type": "optional",
+        },
+        "use_hbp": {
+            "default": "0",
+            "help": "Wether to use hbp routine instead of the backprojector from fbp ",
+            "validator": boolean_validator,
+            "type": "optional",
+        },
+        "fan_source_distance_meters": {
+            "default": 1.0e9,
+            "help": "For HBP, for the description of the fan geometry, the source to axis distance. Defaults to a large value which implies parallel geometry",
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "start_z_mm": {
+            "default": "0",
+            "help": help_start_end_z,
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "end_z_mm": {
+            "default": "0",
+            "help": " To determine the reconstructed vertical range: the height in millimiters above the stage below which slices are reconstructed ",
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "start_z_fract": {
+            "default": "0",
+            "help": help_start_end_z,
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "end_z_fract": {
+            "default": "0",
+            "help": " To determine the reconstructed vertical range: the height in fractional position between first doable slice and last doable slice  above the stage below which slices are reconstructed ",
+            "validator": float_validator,
+            "type": "optional",
+        },
+        "start_z": {
+            "default": "0",
+            "help": "the first slice of the reconstructed range. Numbered going in the direction of the scan and starting with number zero for the first doable slice",
+            "validator": slice_num_validator,
+            "type": "optional",
+        },
+        "end_z": {
+            "default": "-1",
+            "help": "the "
+            "end"
+            " slice of the reconstructed range. Numbered going in the direction of the scan and starting with number zero for the first doable slice",
+            "validator": slice_num_validator,
+            "type": "optional",
+        },
+    }
+)
+nabu_config["pipeline"].update(
+    {
+        "skip_after_flatfield_dump": {
+            "default": "0",
+            "help": "When the writing of the flatfielded data is activated, if this option is set, then the phase and reconstruction steps are skipped",
+            "validator": boolean_validator,
+            "type": "optional",
+        },
+    }
+)
+nabu_config["reconstruction"].update(
+    {
+        "angular_tolerance_steps": {
+            "default": "3.0",
+            "help": "the angular tolerance, an angular width expressed in units of an angular step, which is tolerated in the criteria for deciding if a slice is reconstructable or not",
+            "validator": float_validator,
+            "type": "advanced",
+        },
+        "redundancy_angle_deg": {
+            "default": "0",
+            "help": "Can be 0,180 or 360. If there are dead detector regions (notably scintillator junction (stripes) which need to be complemented at +-360 for local tomo or +- 180 for conventional tomo. This may have an impact on the doable vertical span (you can check it with the --dry-run 1 option)",
+            "validator": float_validator,
+            "type": "advanced",
+        },
+        "enable_halftomo": {
+            "default": "0",
+            "help": "nabu-helical applies the same treatment for half-tomo as for full-tomo. Always let this key to zero",
+            "validator": boolean_validator,
+            "type": "advanced",
+        },
+        "helical_halftomo": {
+            "default": "1",
+            "help": "Wether to consider doable slices those which are contributed by an angular span greater or equal to 360, instead of just 180 or more",
+            "validator": boolean_validator,
+            "type": "advanced",
+        },
+    }
+)

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/pipeline/helical/processconfig.py

@@ -0,0 +1,62 @@
+from .nabu_config import nabu_config, renamed_keys
+from .dataset_validator import HelicalDatasetValidator
+from ..fullfield import processconfig as ff_processconfig
+from ...resources import dataset_analyzer
+
+
+class ProcessConfig(ff_processconfig.ProcessConfig):
+    default_nabu_config = nabu_config
+    config_renamed_keys = renamed_keys
+    _use_horizontal_translations = False
+
+    def _configure_save_steps(self):
+        self._dump_sinogram = False
+        steps_to_save = self.nabu_config["pipeline"]["save_steps"]
+        if steps_to_save in (None, ""):
+            self.steps_to_save = []
+            return
+        steps_to_save = [s.strip() for s in steps_to_save.split(",")]
+        for step in self.processing_steps:
+            step = step.strip()
+            if step in steps_to_save:
+                self.processing_options[step]["save"] = True
+                self.processing_options[step]["save_steps_file"] = self.get_save_steps_file(step_name=step)
+        # "sinogram" is a special keyword, not explicitly in the processing steps
+        if "sinogram" in steps_to_save:
+            self._dump_sinogram = True
+            self._dump_sinogram_file = self.get_save_steps_file(step_name="sinogram")
+        self.steps_to_save = steps_to_save
+
+    def _update_dataset_info_with_user_config(self):
+        super()._update_dataset_info_with_user_config()
+
+        self._get_translation_file("reconstruction", "z_per_proj_file", "z_per_proj", last_dim=1)
+        self._get_translation_file("reconstruction", "x_per_proj_file", "x_per_proj", last_dim=1)
+
+    def _get_user_sino_normalization(self):
+        """is called by the base class but it is not used in helical"""
+        pass
+
+    def _coupled_validation(self):
+        self.logger.debug("Doing coupled validation")
+        self._dataset_validator = HelicalDatasetValidator(self.nabu_config, self.dataset_info)
+        for what in ["rec_params", "rec_region", "binning", "subsampling_factor"]:
+            setattr(self, what, getattr(self._dataset_validator, what))
+            print(what, self._dataset_validator)
+
+    def _browse_dataset(self, dataset_info):
+        """
+        Browse a dataset and builds a data structure with the relevant information.
+        """
+        self.logger.debug("Browsing dataset")
+        if dataset_info is not None:
+            self.dataset_info = dataset_info
+        else:
+            self.dataset_info = dataset_analyzer.analyze_dataset(
+                self.nabu_config["dataset"]["location"],
+                extra_options={
+                    "exclude_projections": self.nabu_config["dataset"]["exclude_projections"],
+                    "hdf5_entry": self.nabu_config["dataset"]["hdf5_entry"],
+                },
+                logger=self.logger,
+            )