updated particle picking plotting to handle multiple metadata files a…

…nd added example scripts

scripts/plot_ctf_example.sh

@@ -3,19 +3,19 @@
 EXECUTABLE=$"roodmus"
 SUBROUTINE=$" plot_ctf"
 
-CONFIG_DIR=/path/to/config/files/dir
-NUM_UGRAPHS=5
-META_FILE=/path/to/metafile
-PLOT_DIR=/path/to/output/files/dir
+CONFIG_DIR=path/to/config/files
+META_FILE=path/to/meta/file
+JOB_TYPES="job019_extraction"
+PLOT_DIR=path/to/plot/directory
 PLOT_TYPES="scatter" # "scatter" or "per-particle-scatter"
 DPI=300
 
 $EXECUTABLE $SUBROUTINE \
     --verbose \
     --tqdm \
     --config_dir $CONFIG_DIR \
-    --num_ugraphs $NUM_UGRAPHS \
     --meta_file $META_FILE \
+    --job_types $JOB_TYPES \
     --plot_dir $PLOT_DIR \
     --plot_types $PLOT_TYPES \
     --dpi $DPI

scripts/plot_picking_example.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+EXECUTABLE=$"roodmus"
+SUBROUTINE=$" plot_picking"
+
+CONFIG_DIR=path/to/config/files
+NUM_UGRAPHS=1
+META_FILE="path/to/meta/file1 \
+    path/to/meta/file2 "
+JOB_TYPES="job012_extraction job020_selection"
+PLOT_DIR=path/to/plot/directory
+PLOT_TYPES="label_truth label_picked label_truth_and_picked label_matched_and_unmatched precision boundary overlap"
+BOX_WIDTH=16
+BOX_HEIGHT=16
+PARTICLE_DIAMETER=100
+DPI=300
+
+$EXECUTABLE $SUBROUTINE \
+    --verbose \
+    --tqdm \
+    --config_dir $CONFIG_DIR \
+    --num_ugraphs $NUM_UGRAPHS \
+    --meta_file $META_FILE \
+    --job_types $JOB_TYPES \
+    --plot_dir $PLOT_DIR \
+    --plot_types $PLOT_TYPES \
+    --dpi $DPI

scripts/write_starfile_example.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+
+EXECUTABLE=$"roodmus"
+SUBROUTINE=$" write_starfile"
+
+INPUT_CSV=path/to/input/csv/file
+TYPE=coordinate_star
+OUTPUT_DIR=path/to/output/directory
+UGRAPH_DIR=Micrographs
+PIXEL_SIZE=1
+
+$EXECUTABLE $SUBROUTINE \
+    --verbose \
+    --tqdm \
+    --input_csv $INPUT_CSV \
+    --type $TYPE \
+    --output_dir $OUTPUT_DIR \
+    --ugraph_dir $UGRAPH_DIR \
+    --pixel_size $PIXEL_SIZE
+
+INPUT_CSV=path/to/input/csv/file
+TYPE=data_star
+OUTPUT_DIR=path/to/output/directory
+UGRAPH_DIR=Micrographs
+PIXEL_SIZE=1
+OPTICS_GROUP_NAME=opticsGroup1
+OPTICS_GROUP=1
+MTF_FILENAME=mtf_300kV.star
+MICROGRAPH_ORIGINAL_PIXEL_SIZE=1.0
+VOLTAGE=300.0
+SPHERICAL_ABERRATION=2.7
+AMPLITUDE_CONTRAST=0.1
+IMAGE_PIXEL_SIZE=1.0
+IMAGE_SIZE=128
+IMAGE_DIMENSIONALITY=2
+CTF_DATA_ARE_CTF_PREMULTIPLIED=0
+
+$EXECUTABLE $SUBROUTINE \
+    --verbose \
+    --tqdm \
+    --input_csv $INPUT_CSV \
+    --type $TYPE \
+    --output_dir $OUTPUT_DIR \
+    --ugraph_dir $UGRAPH_DIR \
+    --pixel_size $PIXEL_SIZE \
+    --optics_group_name $OPTICS_GROUP_NAME \
+    --optics_group $OPTICS_GROUP \
+    --mtf_filename $MTF_FILENAME \
+    --micrograph_original_pixel_size $MICROGRAPH_ORIGINAL_PIXEL_SIZE \
+    --voltage $VOLTAGE \
+    --spherical_aberration $SPHERICAL_ABERRATION \
+    --amplitude_contrast $AMPLITUDE_CONTRAST \
+    --image_pixel_size $IMAGE_PIXEL_SIZE \
+    --image_size $IMAGE_SIZE \
+    --image_dimensionality $IMAGE_DIMENSIONALITY \
+    --ctf_data_are_ctf_premultiplied $CTF_DATA_ARE_CTF_PREMULTIPLIED
+
+

src/roodmus/analysis/extract_particles.py

@@ -60,6 +60,12 @@ def add_arguments(parser):
         type=str,
         default="particles",
     )
+    parser.add_argument(
+        "--file_type",
+        help="File type of the micrographs. Default 'mrcs'",
+        type=str,
+        default="mrcs",
+    )
     parser.add_argument(
         "--tqdm",
         help="Use tqdm progress bar. Default False",
@@ -100,6 +106,24 @@ def get_particle(
     return particle
 
 
+def save_particle_stack(
+    particle_stack: np.ndarray, particle_dir: str, file_type: str
+):
+    particle_file = os.path.join(
+        args.particle_dir,
+        "particle_stack." + file_type,
+    )
+
+    if file_type == "mrcs" or file_type == "mrc":
+        with mrcfile.new(particle_file, overwrite=True) as mrc:
+            mrc.set_data(np.float32(particle_stack))
+            mrc.set_image_stack()
+            mrc.update_header_from_data()
+
+    elif file_type == "tif" or file_type == "tiff":
+        tifffile.imwrite(particle_file.replace(".mrc", ".tif"), particle_stack)
+
+
 def main(args):
     if args.mrc_dir is None:
         args.mrc_dir = args.config_dir
@@ -152,17 +176,8 @@ def main(args):
                 print(f"particle stack shape: {particle_stack.shape}")
 
             # save the particle stack
-            particle_file = os.path.join(
-                args.particle_dir,
-                "particle_stack.mrc",
-            )
-
-            with mrcfile.new(particle_file, overwrite=True) as mrc:
-                mrc.set_data(np.float32(particle_stack))
-                mrc.set_image_stack()
-                mrc.update_header_from_data()
-            tifffile.imwrite(
-                particle_file.replace(".mrc", ".tif"), particle_stack
+            save_particle_stack(
+                particle_stack, args.particle_dir, args.file_type
             )