#33 Updated 0200 to use argparse

src/processing_steps/0200_generate_byte_hdf5.py

@@ -1,19 +1,21 @@
 #! /usr/bin/python3
 '''
 Byte-per-voxel HDF5 files for complete multi-scan tomograms
-Format
-/subvolume_dimensions:  int(n,3).      For each of the n component scans, the sub-volume dimensions (nz,ny,nx)
-/subvolume_range:     float(n,2).      For each of the n component scane, the value range (vmin,vmax)
-/subvolume_metadata:  group            Attributes are info from ESRF XML-file describing original data
-/voxels:              uint8(Nz,Ny,Nx). Nz = sum(scan_dimensions[:,0]), ny = minimum(subvolume_dimensions[:,1]), nx = minimum(subvolume_dimensions[:,2])
+
+Format:
+/subvolume_dimensions: int(n,3).         For each of the n component scans, the sub-volume dimensions (nz,ny,nx)
+/subvolume_range:      float(n,2).       For each of the n component scane, the value range (vmin,vmax)
+/subvolume_metadata:   group             Attributes are info from ESRF XML-file describing original data
+/voxels:               uint8(Nz,Ny,Nx).  Nz = sum(scan_dimensions[:,0]), ny = minimum(subvolume_dimensions[:,1]), nx = minimum(subvolume_dimensions[:,2])
 '''
 import sys
 sys.path.append(sys.path[0]+"/../")
 
 from config.paths import hdf5_root as hdf5_root, esrf_implants_root
 import h5py
+from lib.py.commandline_args import default_parser
 from lib.py.esrf_read import *
-from lib.py.helpers import commandline_args, generate_cylinder_mask, normalize
+from lib.py.helpers import generate_cylinder_mask, normalize
 import numpy as np
 import os.path
 import pathlib
@@ -22,18 +24,17 @@
 NA = np.newaxis
 
 if __name__ == "__main__":
-    sample, chunk_length, use_bohrium, xml_root, verbose = commandline_args({
-        "sample" : "<required>",
-        "chunk_length" : 256,
-        "use_bohrium" : True,
-        "xml_root" : esrf_implants_root,
-        "verbose" : 1
-    })
-
-    if verbose >= 1: print(f"data_root={xml_root}")
-
-    subvolume_xmls       = readfile(f"{xml_root}/index/{sample}.txt")
-    subvolume_metadata   = [esrf_read_xml(f"{xml_root}/{xml.strip()}") for xml in subvolume_xmls]
+    argparser = default_parser(description=__doc__)
+    argparser.add_argument('--use_bohrium', action='store_true',
+        help='Toggles whether to use Bohrium for processing.')
+    argparser.add_argument('--xml_root', action='store', type=str, default=esrf_implants_root,
+        help='The root directory of the ESRF 2013 dataset.')
+    args = argparser.parse_args()
+
+    if args.verbose >= 1: print(f"data_root={args.xml_root}")
+
+    subvolume_xmls       = readfile(f"{args.xml_root}/index/{args.sample}.txt")
+    subvolume_metadata   = [esrf_read_xml(f"{args.xml_root}/{xml.strip()}") for xml in subvolume_xmls]
     subvolume_dimensions = np.array([(int(m['sizez']), int(m['sizey']), int(m['sizex'])) for m in subvolume_metadata])
     subvolume_range      = np.array([(float(m['valmin']), float(m['valmax'])) for m in subvolume_metadata])
 
@@ -44,23 +45,23 @@
     # 2) top or bottom can have important info (depending on orientation of scan)
     (Nz,Ny,Nx)  = (np.sum(subvolume_dimensions[:,0]), np.min(subvolume_dimensions[:,1]&~31), np.min(subvolume_dimensions[:,2]&~31))
 
-    if verbose >= 1:
+    if args.verbose >= 1:
         for i in range(len(subvolume_metadata)):
-            print(f"{i} {sample}/{subvolume_metadata[i]['experiment']}: {subvolume_range[i]}")
+            print(f"{i} {args.sample}/{subvolume_metadata[i]['experiment']}: {subvolume_range[i]}")
         print((global_vmin, global_vmax), (Nz,Ny,Nx))
         print(subvolume_dimensions)
         print(subvolume_range)
 
-    msb_filename = f"{hdf5_root}/hdf5-byte/msb/{sample}.h5"
-    lsb_filename = f"{hdf5_root}/hdf5-byte/lsb/{sample}.h5"
+    msb_filename = f"{hdf5_root}/hdf5-byte/msb/{args.sample}.h5"
+    lsb_filename = f"{hdf5_root}/hdf5-byte/lsb/{args.sample}.h5"
 
     # Make sure directory exists
     outdir = os.path.dirname(msb_filename)
     pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
     outdir = os.path.dirname(lsb_filename)
     pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
 
-    if verbose >= 1: print(f"Writing {msb_filename} and {lsb_filename}")
+    if args.verbose >= 1: print(f"Writing {msb_filename} and {lsb_filename}")
     h5file_msb = h5py.File(msb_filename,"w")
     h5file_lsb = h5py.File(lsb_filename,"w")
 
@@ -93,36 +94,36 @@
         (nz, ny, nx)   = subvolume_dimensions[i]
         (sy, sx)       = ((ny-Ny)//2 + ((ny-Ny)%2), (nx-Nx)//2 + ((nx-Nx)%2))
         (ey, ex)       = (ny-(ny-Ny)//2, nx-(nx-Nx)//2)
-        if verbose >= 1: print((sy,ey), (sx,ex))
+        if args.verbose >= 1: print((sy,ey), (sx,ex))
 
-        chunk = np.zeros((chunk_length, Ny, Nx), dtype=np.uint16)
-        for z in range(0, nz, chunk_length):
-            chunk_end = min(z+chunk_length, nz)
+        chunk = np.zeros((args.chunk_length, Ny, Nx), dtype=np.uint16)
+        for z in range(0, nz, args.chunk_length):
+            chunk_end = min(z+args.chunk_length, nz)
 
             region = [[sx, sy, z], [ex, ey, chunk_end]]
-            if verbose >= 1: print(f"Reading chunk {z+z_offset}:{chunk_end+z_offset} ({i}-{z}), region={region}")
+            if args.verbose >= 1: print(f"Reading chunk {z+z_offset}:{chunk_end+z_offset} ({i}-{z}), region={region}")
 
             slab_data = esrf_edfrange_to_bh(subvolume_info,region)
-            if verbose >= 1: print(f"Chunk shape: {slab_data.shape}")
-            if verbose >= 1: print("Max value before masking:", slab_data.max())
+            if args.verbose >= 1: print(f"Chunk shape: {slab_data.shape}")
+            if args.verbose >= 1: print("Max value before masking:", slab_data.max())
 
             slab_data *= mask[NA,:,:]
-            if verbose >= 1: print("Max value after masking:", slab_data.max())
+            if args.verbose >= 1: print("Max value after masking:", slab_data.max())
 
             chunk[:chunk_end-z] = normalize(slab_data, (global_vmin,global_vmax))
-            if verbose >= 1: print("Max value after normalizing:", chunk.max())
+            if args.verbose >= 1: print("Max value after normalizing:", chunk.max())
 
             chunk_msb = ((chunk[:chunk_end-z] >> 8) & 0xff).astype(np.uint8)
             chunk_lsb = ( chunk[:chunk_end-z]       & 0xff).astype(np.uint8)
 
-            if verbose >= 1:
-                print(f"Writing {sample} MSB slice {z+z_offset}:{chunk_end+z_offset} ({i}-{z})")
+            if args.verbose >= 1:
+                print(f"Writing {args.sample} MSB slice {z+z_offset}:{chunk_end+z_offset} ({i}-{z})")
                 print("chunk_msb.max: ", chunk_msb.max())
                 print("chunk_msb.copy2numpy().max: ", chunk_msb.max())
             h5tomo_msb[z_offset+z:z_offset+chunk_end] = chunk_msb[:]
 
-            if verbose >= 1:
-                print(f"Writing {sample} LSB slice {z+z_offset}:{chunk_end+z_offset} ({i}-{z})")
+            if args.verbose >= 1:
+                print(f"Writing {args.sample} LSB slice {z+z_offset}:{chunk_end+z_offset} ({i}-{z})")
                 print("chunk_lsb.max: ", chunk_lsb.max())
                 print("chunk_lsb.copy2numpy().max: ", chunk_lsb.max())
             h5tomo_lsb[z_offset+z:z_offset+chunk_end] = chunk_lsb[:]