add init_seq_func to focussingSequence function. Add 'start_idx' key to sequenc control dictionary (see getFocusSequencePars). Rewrite aps

focus_app.py

@@ -6,9 +6,10 @@
 import OBSUTILS as obsutil
 import sys
 import numpy as np
+import pathlib as pl
 
 
-def focussing_app(parser, set_focus, get_image):
+def focussing_app(parser, init_seq_func, set_focus_func, get_image_func):
     """
     Focussing sequence standard application skeleton
 
@@ -109,13 +110,29 @@ def focussing_app(parser, set_focus, get_image):
     if args.guess:  # rough focus estimation
         if args.verbose:
             print("\trough focus estimation ...")
+
+        # add '_rough' suffixes
+        seq_rough_kwds = seq_kwds.copy()
+        if seq_rough_kwds["focus_curve_filename"] is not None:
+            pt = pl.Path(seq_rough_kwds["focus_curve_filename"])
+            seq_rough_kwds["focus_curve_filename"] = str(
+                pt.with_stem(pt.stem + "_rough")
+            )
+
+        if seq_rough_kwds["result_data_filename"] is not None:
+            pt = pl.Path(seq_rough_kwds["result_data_filename"])
+            seq_rough_kwds["result_data_filename"] = str(
+                pt.with_stem(pt.stem + "_rough")
+            )
+
         result = obsutil.focussingSequence(
             [focus_start, focus_stop],
-            set_focus,
+            init_seq_func,
-            get_image,
+            set_focus_func,
+            get_image_func,
             None,
             sys.stdout,
-            **seq_kwds
+            **seq_rough_kwds
         )
 
         if result["ret_code"] != 0:
@@ -130,7 +147,7 @@ def focussing_app(parser, set_focus, get_image):
 
         if args.verbose:
             print(
-                "\testimate guess focus position in range [{:g},{:g}]".format(
+                "\testimate guess focus position in range of [{:g},{:g}]".format(
                     focus_start, focus_stop
                 )
             )
@@ -138,8 +155,9 @@ def focussing_app(parser, set_focus, get_image):
     if np.isfinite(args.focus_step):
         result = obsutil.focussingSequence(
             [focus_start, focus_stop, focus_step],
-            set_focus,
+            init_seq_func,
-            get_image,
+            set_focus_func,
+            get_image_func,
             None,
             sys.stdout,
             **seq_kwds
@@ -147,8 +165,9 @@ def focussing_app(parser, set_focus, get_image):
     else:
         result = obsutil.focussingSequence(
             [focus_start, focus_stop],
-            set_focus,
+            init_seq_func,
-            get_image,
+            set_focus_func,
+            get_image_func,
             None,
             sys.stdout,
             **seq_kwds
@@ -160,7 +179,7 @@ def focussing_app(parser, set_focus, get_image):
     if not args.do_not_set:
         if args.verbose:
             print("\n\tSet focus to the best value ...", end="")
-            set_focus(result["focus_value"])
+            set_focus_func(result["focus_value"])
             print("\tOK")
 
     if args.verbose:

focus_seq_FLI.py

@@ -20,6 +20,26 @@ import pathlib as pl
 # --- FLI-hardware related (ROBOTEL variant)
 
 
+def init_seq(seq_kwds):
+    # remove extension as Eddy's 'fli_control' add hardcoded '.fit'
+    pt = pl.Path(seq_kwds["root_filename"]).with_suffix("")
+    seq_kwds["root_filename"] = str(pt)
+
+    #
+    #
+
+    foc_files = list(
+        pt.absolute().parent.glob("{}_[0-9][0-9][0-9][0-9].fit".format(pt.stem))
+    )
+
+    seq_kwds["start_idx"] = 1
+    N = len(foc_files)
+    if N > 0:
+        seq_kwds["start_idx"] = N
+
+    return 0
+
+
 def set_focus(foc_val):
     cmd = ["fli_control", "-g", str(int(foc_val))]
     ret = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
@@ -55,6 +75,6 @@ if __name__ == "__main__":
         description="FLI CCD and focuser hardware: focussing sequence implementation. It is assumed that 'fli_control' software is installed in the OS.",
     )
 
-    ret = focussing_app(parser, set_focus, get_image)
+    ret = focussing_app(parser, init_seq, set_focus, get_image)
 
     sys.exit(ret)

focus_seq_Z1000_IXon.py

@@ -17,6 +17,22 @@ import argparse as ap
 import subprocess as sp
 import numpy as np
 import socket
+import pathlib as pl
+
+
+def init_seq(seq_kwds):
+    pt = pl.Path(seq_kwds["root_filename"])
+
+    foc_files = list(
+        pt.absolute().parent.glob("{}_[0-9][0-9][0-9][0-9].fit".format(pt.stem))
+    )
+
+    seq_kwds["start_idx"] = 1
+    N = len(foc_files)
+    if N > 0:
+        seq_kwds["start_idx"] = N
+
+    return 0
 
 
 def set_focus(foc_val):
@@ -51,6 +67,6 @@ if __name__ == "__main__":
         description="Zeiss-1000 and Andor Ixon EMCCD hardware: focussing sequence implementation.",
     )
 
-    ret = focussing_app(parser, set_focus, get_image)
+    ret = focussing_app(parser, init_seq, set_focus, get_image)
 
     sys.exit(ret)

focus_utils.py

@@ -84,7 +84,8 @@ def getFocusSequencePars(**user_kwds):
         "focus_start": None,
         "focus_stop": None,
         "focus_step": None,
-        "root_filename": "focus.fit",
+        "root_filename": "focus.fits",
+        "start_idx": 1,  # start index of files in sequence
         "acq_per_value": 1,  # number of acquisitions per focus value
         "exp_time": 10,  # exposure time in seconds
         "set_to_best": True,  # set focus to the best value
@@ -283,6 +284,7 @@ def computeFocus(
 
 def focussingSequence(
     focus_range,
+    init_seq_func,
     set_focus_func,
     get_image_func,
     max_wks=None,
@@ -295,6 +297,9 @@ def focussingSequence(
 
         focus_range: [start, stop] (7 points)
                      or [start, stop, step]
+        init_seq_func: a function with signature:
+                        init_seq_func(seq_kwds),
+                        where seq_kwds - sequence control dictionary (see getFocusSequencePars function)
         set_focus_func: a function of signature:
                           set_focus_func(foc_val)
         get_image_func: a function of signature:
@@ -373,6 +378,8 @@ def focussingSequence(
 
     seq_kwds = getFocusSequencePars(**kwds)
 
+    init_seq_func(seq_kwds)
+
     if seq_kwds["acq_per_value"] > 1:
         focus_value = (
             np.array([focus_value] * seq_kwds["acq_per_value"]).transpose().flatten()
@@ -380,18 +387,19 @@ def focussingSequence(
 
     rname = pt.Path(seq_kwds["root_filename"]).absolute()
 
-    dir = rname.parent
+    # dir = rname.parent
-    fname = rname.stem
+    # fname = rname.stem
-    file_ext = rname.suffix
+    # file_ext = rname.suffix
-    if file_ext == "":
+    # if file_ext == "":
-        file_ext = ".fit"
+    #     file_ext = ".fit"
 
     futures = []
     flux_rad = []
 
     executor = ProcessPoolExecutor(max_workers=max_wks)
 
-    i_foc = 1
+    i_foc = seq_kwds["start_idx"]
+
     ret_code = 0
     for foc_val in focus_value:
         print(log_ident, file=log_output, end="")
@@ -410,8 +418,10 @@ def focussingSequence(
         else:
             print("OK", file=log_output, flush=True)
 
-        filename = "{}_{:04d}{}".format(fname, i_foc, file_ext)
+        # filename = "{}_{:04d}{}".format(fname, i_foc, file_ext)
-        full_filename = str(pt.Path.joinpath(dir, pt.Path(filename)))
+        # full_filename = str(pt.Path.joinpath(dir, pt.Path(filename)))
+
+        full_filename = str(rname.with_stem("{}_{:04d}", rname.stem, i_foc))
 
         print(log_ident, file=log_output, end="")
         print(
@@ -603,9 +613,9 @@ def getFocussingSequenceCmdlinePars(parser):
 
     parser.add_argument(
         "--foc-file",
-        help="Rootname of output focussing images. Default is 'focus.fit'.",
+        help="Rootname of output focussing images. Default is 'focus.fits'.",
         type=str,
-        default="focus.fit",
+        default="focus.fits",
     )
 
     parser.add_argument(
@@ -725,7 +735,7 @@ def parsFocussingSequenceCmdlinePars(parser_args, parser_msg=[]):
         parser_msg.append("Invalid '--foc_file' argument! Use of defaul value!")
 
     kwds["root_filename"] = (
-        parser_args.foc_file if parser_args.foc_file != "" else "focus.fit"
+        parser_args.foc_file if parser_args.foc_file != "" else "focus.fits"
     )
 
     if parser_args.repeat <= 0: