nabu 2024.2.0rc3__tar.gz → 2024.2.1__tar.gz

{nabu-2024.2.0rc3/nabu.egg-info → nabu-2024.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc3
+Version: 2024.2.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2024.2.0-rc3"
+__version__ = "2024.2.1"
 __nabu_modules__ = [
     "app",
     "cuda",

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/app/cli_configs.py

@@ -37,7 +37,7 @@ BootstrapConfig = {
         "default": "",
     },
     "template": {
-        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
+        "help": "Use a template configuration file. Available are: id19_pag, id16_holo, id16_ctf, id16a_fluo, bm05_pag. You can also define your own templates via the NABU_TEMPLATES_PATH environment variable.",
         "default": "",
     },
     "helical": {"help": "Prepare configuration file for helical", "default": 0, "required": False, "type": int},

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/estimation/cor.py

@@ -239,7 +239,7 @@ class CenterOfRotationSlidingWindow(CenterOfRotation):
                 win_2_start = img_width // 2 - window_shift
         else:
             abs_pos = int(side + img_width // 2)
-            window_fraction = 0.2  # Hard-coded ?
+            window_fraction = 0.1  # Hard-coded ?
 
             window_width = round(window_fraction * img_width)
             window_shift = window_width // 2

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/pipeline/estimators.py

@@ -243,13 +243,13 @@ class CORFinder(CORFinderBase):
         # All find_shift() methods in self.search_methods have the same API with "img_1" and "img_2"
         cor_exec_kwargs = update_func_kwargs(self.cor_finder.find_shift, self.cor_options)
         cor_exec_kwargs["return_relative_to_middle"] = False
-        # FIXME
+        # ----- FIXME -----
         # 'self.cor_options' can contain 'side="from_file"', and we should not modify it directly
         # because it's entered by the user.
         # Either make a copy of self.cor_options, or change the inspect() mechanism
-        if cor_exec_kwargs["side"] == "from_file":
+        if cor_exec_kwargs.get("side", None) == "from_file":
             cor_exec_kwargs["side"] = self._lookup_side or "center"
-        #
+        # ------
         if self._lookup_side is not None:
             cor_exec_kwargs["side"] = self._lookup_side
         self.logger.debug("%s.find_shift(%s)" % (self.cor_finder.__class__.__name__, str(cor_exec_kwargs)))

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/pipeline/fullfield/chunked.py

@@ -668,7 +668,10 @@ class ChunkedPipeline:
             "jpeg2000_compression_ratio": options["jpeg2000_compression_ratio"],
             "float_clip_values": options["float_clip_values"],
             "tiff_single_file": options.get("tiff_single_file", False),
-            "single_output_file_initialized": getattr(self.process_config, "single_output_file_initialized", False),
+            "single_output_file_initialized": getattr(
+                self.process_config, "single_output_file_initialized", False
+            ),  # COMPAT.
+            "writer_initialized": getattr(self.process_config, "_writer_initialized", False),
             "raw_vol_metadata": {"voxelSize": self.dataset_info.pixel_size},  # legacy...
         }
         writer_extra_options.update(extra_options)
@@ -853,7 +856,8 @@ class ChunkedPipeline:
         self.writer.write_data(data)
         self.logger.info("Wrote %s" % self.writer.fname)
         self._write_histogram()
-        self.process_config.single_output_file_initialized = True
+        self.process_config.single_output_file_initialized = True  # COMPAT.
+        self.process_config._writer_initialized = True
 
     def _write_histogram(self):
         if "histogram" not in self.processing_steps:

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/pipeline/fullfield/processconfig.py

@@ -465,7 +465,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "chunk":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "chunk",
             }
@@ -513,7 +513,7 @@ class ProcessConfig(ProcessConfigBase):
         if self.get_radios_rotation_mode() == "full":
             tasks.append("tilt_correction")
             options["tilt_correction"] = {
-                "angle": nabu_config["preproc"]["tilt_correction"] or dataset_info.detector_tilt,
+                "angle": dataset_info.detector_tilt,
                 "center": nabu_config["preproc"]["rotate_projections_center"],
                 "mode": "full",
             }

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/pipeline/fullfield/reconstruction.py

@@ -253,7 +253,7 @@ class FullFieldReconstructor:
         if self.process_config.processing_options.get("phase", {}).get("method", None) == "CTF":
             force_grouped_mode = True
             msg = "CTF phase retrieval needs to process full radios"
-        if self.process_config.processing_options.get("tilt_correction", {}).get("angle", 0) > 15:
+        if (self.process_config.dataset_info.detector_tilt or 0) > 15:
             force_grouped_mode = True
             msg = "Radios rotation with a large angle needs to process full radios"
         if self.process_config.resume_from_step == "sinogram" and force_grouped_mode:

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/pipeline/writer.py

@@ -1,5 +1,6 @@
 from os import path
 from tomoscan.esrf import TIFFVolume, MultiTIFFVolume, EDFVolume, JP2KVolume
+from tomoscan.esrf.volume.singleframebase import VolumeSingleFrameBase
 from ..utils import check_supported, get_num_threads
 from ..resources.logger import LoggerOrPrint
 from ..io.writer import NXProcessWriter, HSTVolVolume, NXVolVolume
@@ -113,6 +114,7 @@ class WriterManager:
         return vol_writer.data_url.file_path()
 
     def _init_writer(self):
+        self._writer_was_already_initialized = self.extra_options.get("writer_initialized", False)
         if self.file_format in ["tiff", "edf", "jp2", "hdf5"]:
             writer_kwargs = {
                 "folder": self.output_dir,
@@ -143,6 +145,11 @@ class WriterManager:
         self._h5_entry = self.metadata.get("entry", "entry")
         self.writer = self._writer_classes[self.file_format](**writer_kwargs)
         self.fname = self.get_fname(self.writer)
+        # In certain cases, tomoscan needs to remove any previous existing volume filess
+        # and avoid calling 'clean_output_data' when writing downstream (for chunk processing)
+        if isinstance(self.writer, VolumeSingleFrameBase):
+            self.writer.skip_existing_data_files_removal = self._writer_was_already_initialized
+        # ---
         if path.exists(self.fname):
             err = "File already exists: %s" % self.fname
             if self.overwrite:

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/resources/dataset_analyzer.py

@@ -52,7 +52,7 @@ class DatasetAnalyzer:
             "output_dir": None,
             "exclude_projections": None,
             "hdf5_entry": None,
-            "nx_version": 1.0,
+            # "nx_version": 1.0,
         }
         # --
         advanced_options.update(extra_options)

{nabu-2024.2.0rc3 → nabu-2024.2.1}/nabu/resources/nxflatfield.py

@@ -35,12 +35,10 @@ def get_frame_possible_urls(dataset_info, user_dir, output_dir):
         else:
             dataurl_default_template = h5scan.REDUCED_DARKS_DATAURLS[0]
 
-        rel_file_path = dataurl_default_template.file_path().format(
-            scan_prefix=dataset_info.dataset_scanner.get_dataset_basename()
-        )
+        rel_file_path = dataurl_default_template.file_path().format(scan_prefix=h5scan.get_dataset_basename())
         return DataUrl(
             file_path=os.path.join(dirname, rel_file_path),
-            data_path=dataurl_default_template.data_path(),
+            data_path=dataurl_default_template.data_path().format(entry=h5scan.entry, index="{index}"),
             data_slice=dataurl_default_template.data_slice(),  # not sure if needed
             scheme="silx",
         )
@@ -144,9 +142,11 @@ def data_url_exists(data_url):
     """
     if not (os.path.isfile(data_url.file_path())):
         return False
+    group_exists = False
     with HDF5File(data_url.file_path(), "r") as f:
-        path_exists = f.get(data_url.data_path(), default=None) is not None
-    return path_exists
+        data_path_without_index = data_url.data_path().split("{")[0]
+        group_exists = f.get(data_path_without_index, default=None) is not None
+    return group_exists
 
 
 # pylint: disable=E1136

{nabu-2024.2.0rc3 → nabu-2024.2.1/nabu.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nabu
-Version: 2024.2.0rc3
+Version: 2024.2.1
 Summary: Nabu - Tomography software
 Author-email: Pierre Paleo <pierre.paleo@esrf.fr>, Henri Payno <henri.payno@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>
 Maintainer-email: Pierre Paleo <pierre.paleo@esrf.fr>