--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_dexela_h5_filesystem.py	Thu Sep 23 21:00:48 2021 +0000
@@ -0,0 +1,140 @@
+import argparse
+import glob
+import os
+
+import numpy as np
+import time
+from datetime import datetime
+
+from hexrd.imageseries import omega
+import pp_dexela
+#from IPython import embed
+
+# =============================================================================
+# USER INPUT
+# =============================================================================
+
+# panel keys to MATCH INSTRUMENT FILE
+panel_keys = ['FF1', 'FF2']
+panel_opts = dict.fromkeys(panel_keys)
+
+# !!!: hard coded options for each dexela for April 2017
+panel_opts['FF1'] = [('add-row', 1944), ('add-column', 1296),('flip', 'v'), ]
+panel_opts['FF2'] = [('add-row', 1944), ('add-column', 1296),('flip', 'h'), ]
+
+# ==================== End Inputs (should not need to alter below this line)
+
+
+
+def process_dexelas(file_names, samp_name, scan_number,
+                    ostart, ostep, num_frames,
+                    panel_opts, threshold):
+    """
+    wrapper for F2 dexela setup
+    """
+    ostop = ostart + num_frames*ostep
+    omw = omega.OmegaWedges(num_frames)
+    omw.addwedge(ostart, ostop, num_frames)
+
+    for file_name in file_names:
+        for key in panel_keys:
+            if key.lower() in file_name:
+                ppd = pp_dexela.PP_Dexela(
+                    file_name,
+                    omw,
+                    panel_opts[key],
+                    panel_id=key,
+                    frame_start=fstart)
+#                embed()
+#                ppd=add_missing_pixel_gap(ppd)
+
+                output_name = samp_name + '_' + \
+                    str(scan_number) + '_' + \
+                    file_name.split('/')[-1].split('.')[0]
+                ppd.save_processed(output_name, threshold)
+                head_tail = os.path.split(file_name)
+                if head_tail[0] is not None:
+                    os.system('cp -p ' + './' + output_name + '* ' + head_tail[0] + ' 2>/dev/null')
+
+if __name__ == '__main__':
+    #
+    #  Run preprocessor
+    #
+    print("Running preprocessor....")
+    parser = argparse.ArgumentParser(
+        description="pre-process double Dexela images from F2")
+
+    parser.add_argument('base_dir',
+                        help="raw data path on chess daq", type=str)
+    parser.add_argument('expt_name',
+                        help="experiment name", type=str)
+    parser.add_argument('samp_name',
+                        help="sample name", type=str)
+    parser.add_argument('scan_number',
+                        help="ff scan number", type=int)
+
+    parser.add_argument('-n', '--num-frames',
+                        help="number of frames to read",
+                        type=int, default=1441)
+    parser.add_argument('-s', '--start-frame',
+                        help="index of first data frame",
+                        type=int, default=4)
+    parser.add_argument('-t', '--threshold',
+                        help="threshold for frame caches",
+                        type=int, default=50)
+    parser.add_argument('-o', '--ome-start',
+                        help="start omega",
+                        type=float, default=0.)
+#    parser.add_argument('-d', '--ome-delta',
+#                        help="delta omega",
+#                        type=float, default=0.2498265093684941)
+
+    parser.add_argument('-e', '--ome-end',
+                        help="end omega",
+                        type=float, default=360.)
+
+
+    args = parser.parse_args()
+
+    # strip args
+    data_dir = args.base_dir
+    expt_name = args.expt_name
+    samp_name = args.samp_name
+    scan_number = args.scan_number
+    num_frames = args.num_frames
+    fstart = args.start_frame
+    threshold = args.threshold
+    ostart = args.ome_start
+    oend = args.ome_end
+    ostep = (oend-ostart)/float(num_frames)
+
+    print("== Running preprocessor .... processing ")
+    now = datetime.now()
+    print(now.strftime("%m/%d/%Y %H:%M:%S"))
+
+    file_names = glob.glob(
+        os.path.join(
+            data_dir,
+            expt_name,
+            samp_name,
+            str(scan_number),
+            'ff',
+            '*.h5')
+    )
+    path = os.path.join(data_dir, expt_name, samp_name, str(scan_number), 'ff', '*.h5')
+    print("path = " + path)
+    for f in file_names:
+        print(f)
+
+    check_files_exist = [os.path.exists(file_name) for file_name in file_names]
+    if not np.all(check_files_exist):
+        raise RuntimeError("files don't exist!")
+
+    process_dexelas(file_names, samp_name, scan_number,
+                    ostart, ostep, num_frames,
+                    panel_opts, threshold)
+    now = datetime.now()
+    print(now.strftime("%m/%d/%Y %H:%M:%S"))
+    print("== End of processing " + " ==")
+    print("                                   ")
+