added command-line interface

Author: bwmr

.github/workflows/ruff.yml

@@ -0,0 +1,10 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+        with:
+            args: --fix

pyproject.toml

@@ -1,5 +1,6 @@
 [build-system]
 requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools.packages.find]
 include = ["sizepicker"]

sizepicker/interface.py

@@ -0,0 +1,141 @@
+from pathlib import Path
+
+import click
+
+from .picker import Picker
+
+
+@click.command()
+@click.option(
+    "--radius",
+    default=80,
+    show_default=True,
+    help="Particle radius [A].")
+@click.option(
+    "--angpix",
+    default=None,
+    type=float,
+    show_default=True,
+    help="Override pixelsize in header [A/pix].")
+@click.option(
+    "--contamination_binning",
+    default=16,
+    show_default=True,
+    help="Binning used to filter out contaminations.")
+@click.option(
+    "--gaussian_cont",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Smooth background by subtracting gaussian-filtered tomogram.")
+@click.option(
+    "--sigma_cont",
+    default=300,
+    show_default=True,
+    help="If smoothing background, apply gaussian filter with this sigma [A].")
+@click.option(
+    "--stdtimes_cont",
+    default=2.5,
+    show_default=True,
+    help="Voxels this many SD below mean are considered contamination.")
+@click.option(
+    "--minsize_cont",
+    default=50,
+    show_default=True,
+    help="Keep only contaminations of this size and above [binned px].")
+@click.option(
+    "--dilate_cont",
+    default=200,
+    show_default=True,
+    help="Dilate contamination mask by this much [A].")
+@click.option(
+    "--radius_times",
+    default=4,
+    show_default=True,
+    help="Picks can be this close together [particle radii].")
+@click.option(
+    "--inhibit",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Use more elaborate algorithm to get more picks.")
+@click.option(
+    "--detection_z",
+    default=200,
+    show_default=True,
+    help="Only consider picks in a central slab of the volume of this extent [px].")
+@click.option(
+    "--stdtimes_pick",
+    default=1.5,
+    show_default=True,
+    help="Only consider picks with a central SD this many SD above mean.")
+@click.option(
+    "--remove_edge",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Only keep particles with a higher foreground than background SD.")
+@click.argument(
+    "tomograms",
+    nargs=-1,
+    type=click.Path(exists=True))
+@click.argument(
+    "output_dir",
+    nargs=1,
+    type=click.Path(writable=True, dir_okay=True))
+def cli(radius,
+        angpix,
+        contamination_binning,
+        gaussian_cont,
+        sigma_cont,
+        stdtimes_cont,
+        minsize_cont,
+        dilate_cont,
+        radius_times,
+        inhibit,
+        detection_z,
+        stdtimes_pick,
+        remove_edge,
+        tomograms,
+        output_dir):
+    """Pick particles based on diameter.
+
+    Takes tomograms as input. Writes all outputs to output_dir.
+
+    """
+    for tomo in tomograms:
+
+        tomo = Path(tomo)
+
+        print("working on")
+
+        p = Picker(tomo,
+                   output_dir,
+                   radius,
+                   contamination_binning,
+                   angpix)
+
+        mask = p.getcont(gaussian_cont,
+                         sigma_cont,
+                         stdtimes_cont,
+                         minsize_cont,
+                         dilate_cont)
+
+        print("Contamination Mask written to..")
+
+        boxes, particles = p.detect(mask,
+                                    radius_times,
+                                    inhibit,
+                                    detection_z)
+
+        print("Initial Picks")
+
+        metrics, threshold = p.prefilt(particles,
+                                       stdtimes_pick)
+
+        boxs_XYZ = p.filt(boxes,
+               metrics,
+               threshold,
+               remove_edge)
+
+        print(f"Wrote {len(boxs_XYZ)} picks to ...")

sizepicker/picker.py

@@ -1,6 +1,5 @@
 import subprocess
 from pathlib import Path
-from typing import Optional
 
 import mrcfile
 import numpy as np
@@ -61,20 +60,20 @@ def __init__(self,
                  output: Path,
                  radius: int = 100,
                  contamination_binning: int = 1,
-                 override_angpix: Optional(float) = None):
+                 override_angpix: float = None): #noqa: RUF013
 
-        self.name=tomogram.stem
-        self.output=output
-        self.radius=radius
+        self.name = tomogram.stem
+        self.output = output
+        self.radius = radius
         self.contamination_binning = contamination_binning
 
         self.rec = mrcfile.read(tomogram)
 
         if override_angpix is None:
             with mrcfile.mmap(tomogram, mode='r') as f:
-                self.pixelsize=float(f.voxel_size.x)
+                self.pixelsize = float(f.voxel_size.x)
         else:
-            self.pixelsize=override_angpix
+            self.pixelsize = override_angpix
 
         # box size for checking whether pick contains density
         self.tilesize = int(3 * radius / self.pixelsize)
@@ -386,7 +385,11 @@ def filt(self,boxes,particles_metrics,stdthreshold,remove_edge):
         stdthreshold: actual SD threshold, from Picker.prefilt()
         remove_edge: remove particles with higher background than foreground SD?
 
-        Writes out coordinate file in XYZ order to output folder.
+        Returns
+        -------
+        boxs_XYZ: XYZ coordiantes of retained particles.
+
+        Also writes out coordinate file in XYZ order to output folder.
 
         """
         boxs_ZYX = []