app.reconstruct: Check z-region for reconstruction

nabu/resources/cli/reconstruct.py

@@ -31,6 +31,51 @@ def get_subregion(slices_indices, radio_nz):
     return (z_start, z_stop)
 
 
+
+def check_margin(subregion, n_z, logger, min_delta_z=10):
+    delta_z = subregion[-1] - subregion[-2]
+    if delta_z >= min_delta_z:
+        return subregion
+    if n_z < min_delta_z:
+        logger.error("Need at least %d detector rows to perform phase/unsharp properly. Results will probably be inaccurate." % min_delta_z)
+        return (0, n_z)
+    logger.warning("Processing at least 10 detector rows for phase/unsharp")
+    hz1 = min_delta_z // 2
+    hz2 = min_delta_z - hz1
+    zmin, zmax = subregion
+    zmin = max(zmin - hz1, 0)
+    zmax = min(zmax + hz2, n_z)
+    if zmax - zmin < min_delta_z:
+        zmin = max(zmin - hz1, 0)
+        zmax = min(zmax + hz2, n_z)
+    return (zmin, zmax)
+
+
+def get_reconstruction_region(arg_slice, process_config, logger):
+    n_z = process_config.dataset_infos._radio_dims_notbinned[-1]
+    rec_opts = process_config.nabu_config["reconstruction"]
+
+    if arg_slice == "":
+        # This will be handled in future versions by inspecting available memory
+        logger.warning("The argument --slice was not provided. This might result in insufficient memory errors.")
+        subregion = (rec_opts["start_z"], rec_opts["end_z"])
+        #
+    else:
+        subregion = get_subregion(
+            args["slice"],
+            process_config.dataset_infos.radio_dims[-1]
+        )
+    delta_z = subregion[-1] - subregion[-2]
+    # This will be handled in future versions by inspecting available memory
+    if delta_z == n_z:
+        logger.warning("It seems that all the volume will be reconstructed. This will probably result in insufficient memory errors. To avoid this, please provide --slice argument or start_z and end_z in parameters file")
+    steps = process_config.processing_steps
+    if "phase" in steps or "unsharp_mask" in steps:
+        subregion = check_margin(subregion, n_z, logger)
+    #
+    return subregion
+
+
 def main():
     args = parse_params_values(
         ReconstructConfig,
@@ -45,29 +90,20 @@ def main():
         logfile=args["log_file"]
     )
 
-    # For now we need the --slice argument
-    if args["slice"].strip() == "":
-        msg = "Need to provide the --slice argument (ex. --slice 1024 or --slice 0-1024)"
-        logger.fatal(msg)
-        exit(1)
-    #
-
-    subregion = get_subregion(
-        args["slice"],
-        proc.dataset_infos.radio_dims[-1]
-    )
+    subregion = get_reconstruction_region(args["slice"].strip(), proc, logger)
     logger.info("Going to reconstruct slices %s" % str(subregion))
     subregion = (None, None) + subregion
 
     # (hopefully) temporary patch
-    if args["energy"] > 0:
-        logger.warning("Using user-provided energy %.2f keV" % args["energy"])
-        proc.dataset_infos.dataset_scanner._energy = args["energy"]
-        proc.processing_options["phase"]["energy_kev"] = args["energy"]
-    if proc.dataset_infos.energy  < 1e-3 and proc.nabu_config["phase"]["method"] != None:
-        msg = "No information on energy. Cannot retrieve phase. Please use the --energy option"
-        logger.fatal(msg)
-        raise ValueError(msg)
+    if "phase" in proc.processing_steps:
+        if args["energy"] > 0:
+            logger.warning("Using user-provided energy %.2f keV" % args["energy"])
+            proc.dataset_infos.dataset_scanner._energy = args["energy"]
+            proc.processing_options["phase"]["energy_kev"] = args["energy"]
+        if proc.dataset_infos.energy  < 1e-3 and proc.nabu_config["phase"]["method"] != None:
+            msg = "No information on energy. Cannot retrieve phase. Please use the --energy option"
+            logger.fatal(msg)
+            raise ValueError(msg)
     #
 
     if __has_pycuda__: