Allow number of free CPU cores to be set in the GUI (#195)

* expose n_free_cpus parameter to in GUI

* Pass n_free_cpus to worker

brainreg/core/cli.py

@@ -98,7 +98,7 @@ def misc_parse(parser):
         "--n-free-cpus",
         dest="n_free_cpus",
         type=check_positive_int,
-        default=4,
+        default=2,
         help="The number of CPU cores on the machine to leave "
         "unused by the program to spare resources.",
     )

brainreg/napari/register.py

@@ -132,6 +132,7 @@ def brainreg_register():
         smoothing_sigma_floating=-1.0,
         histogram_n_bins_floating=128,
         histogram_n_bins_reference=128,
+        n_free_cpus=2,
         debug=False,
     )
 
@@ -216,6 +217,10 @@ def brainreg_register():
             value=DEFAULT_PARAMETERS["histogram_n_bins_reference"],
             label="histogram_n_bins_reference",
         ),
+        n_free_cpus=dict(
+            value=DEFAULT_PARAMETERS["n_free_cpus"],
+            label="Free CPU cores",
+        ),
         debug=dict(
             value=DEFAULT_PARAMETERS["debug"],
             label="Debug mode",
@@ -245,8 +250,9 @@ def widget(
         grid_spacing: int,
         smoothing_sigma_reference: float,
         smoothing_sigma_floating: float,
-        histogram_n_bins_floating: int,
-        histogram_n_bins_reference: int,
+        histogram_n_bins_floating: float,
+        histogram_n_bins_reference: float,
+        n_free_cpus: int,
         debug: bool,
         reset_button,
         check_orientation_button,
@@ -339,6 +345,8 @@ def widget(
              Number of bins used for the generation of the histograms used
              for the calculation of Normalized Mutual Information on the
              reference image
+        n_free_cpus : int
+            How many CPU cores to leave free
         debug: bool
             Activate debug mode (save intermediate steps).
         check_orientation_button:
@@ -401,7 +409,7 @@ def get_gui_logging_args():
             )
 
         @thread_worker
-        def run():
+        def run(n_free_cpus):
             paths = Paths(pathlib.Path(registration_output_folder))
 
             niftyreg_args = NiftyregArgs(
@@ -438,7 +446,10 @@ def run():
                 scaling,
                 load_parallel,
             ) = initialise_brainreg(
-                atlas_key.value, data_orientation, voxel_sizes
+                atlas_key.value,
+                data_orientation,
+                voxel_sizes,
+                n_free_cpus=n_free_cpus,
             )
 
             additional_images_downsample = get_additional_images_downsample(
@@ -491,7 +502,7 @@ def run():
                 f"{paths.registration_output_folder}"
             )
 
-        worker = run()
+        worker = run(n_free_cpus)
         if not block:
             worker.returned.connect(load_registration_as_layers)
 

brainreg/napari/util.py

@@ -9,9 +9,10 @@
 from tqdm import tqdm
 
 
-def initialise_brainreg(atlas_key, data_orientation_key, voxel_sizes):
+def initialise_brainreg(
+    atlas_key, data_orientation_key, voxel_sizes, n_free_cpus=2
+):
     scaling_rounding_decimals = 5
-    n_free_cpus = 2
     atlas = BrainGlobeAtlas(atlas_key)
     source_space = bg.AnatomicalSpace(data_orientation_key)