fxes. working Zeiss-1000+EMCCD sequence

best_focus.py

@@ -52,4 +52,7 @@ if __name__ == "__main__":
     if args.verbose:
         print("\nALL DONE")
 
+    if not args.verbose:
+        print("best focus value is {:g}".format(result["focus_value"]))
+
     sys.exit(0)

focus_app.py

@@ -125,6 +125,10 @@ def focussing_app(parser, init_seq_func, set_focus_func, get_image_func):
                 pt.with_stem(pt.stem + "_rough")
             )
 
+        # rough estimation: be sure that only a single
+        # acquisition per focus value
+        seq_rough_kwds["acq_per_value"] = 1
+
         result = obsutil.focussingSequence(
             [focus_start, focus_stop],
             init_seq_func,
@@ -141,13 +145,14 @@ def focussing_app(parser, init_seq_func, set_focus_func, get_image_func):
             return result["ret_code"]
 
         # compute precise range start and stop values
-        r = args.num * focus_step / 2.0
+        r = (args.num - 1) * focus_step / 2.0
         focus_start = result["focus_value"] - r
         focus_stop = result["focus_value"] + r
 
         if args.verbose:
+            print("\n\t\t rough focus position: {:g}".format(result["focus_value"]))
             print(
-                "\testimate guess focus position in range of [{:g},{:g}]".format(
+                "\t\testimate guess focus position in range of [{:g},{:g}]".format(
                     focus_start, focus_stop
                 )
             )
@@ -173,16 +178,36 @@ def focussing_app(parser, init_seq_func, set_focus_func, get_image_func):
             **seq_kwds
         )
 
+    if result["ret_code"]:
+        if args.verbose:
+            print(
+                "\tFocussing sequence returned error code: {:g}".format(
+                    result["ret_code"]
+                )
+            )
+            print("\tCannot set best focus value!")
+
+        return result["ret_code"]
+
     if args.verbose:
-        print("\tThe best focus value: {:g}".format(result["focus_value"]))
+        print("\n\tThe best focus value: {:g}".format(result["focus_value"]))
+
+    ret_code = 0
 
     if not args.do_not_set:
         if args.verbose:
             print("\n\tSet focus to the best value ...", end="")
-            set_focus_func(result["focus_value"])
-            print("\tOK")
+
+        ret_code = set_focus_func(result["focus_value"])
+
+        if ret_code:
+            if args.verbose:
+                print("\tFAILED")
+        else:
+            if args.verbose:
+                print("\tOK")
 
     if args.verbose:
         print("DONE.")
 
-    return 0
+    return ret_code

focus_seq_FLI.py

@@ -21,8 +21,8 @@ import pathlib as pl
 
 
 def init_seq(seq_kwds):
-    # remove extension as Eddy's 'fli_control' add hardcoded '.fit'
-    pt = pl.Path(seq_kwds["root_filename"]).with_suffix("")
+    # replace extension since Eddy's 'fli_control' adds hardcoded '.fit'
+    pt = pl.Path(seq_kwds["root_filename"]).with_suffix(".fit")
     seq_kwds["root_filename"] = str(pt)
 
     #
@@ -35,12 +35,22 @@ def init_seq(seq_kwds):
     seq_kwds["start_idx"] = 1
     N = len(foc_files)
     if N > 0:
-        seq_kwds["start_idx"] = N
+        max = 0
+        for fname in foc_files:
+            inum = int(fname.stem.split("_")[1])
+            if inum > max:
+                max = inum
+
+        seq_kwds["start_idx"] = max + 1
 
     return 0
 
 
 def set_focus(foc_val):
+    if foc_val < 0:
+        print("INVALID FLI-FOCUSER VALUE! IT MUST BE NON-NEGATIVE VALUE!")
+        return -1
+
     cmd = ["fli_control", "-g", str(int(foc_val))]
     ret = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
     return ret.returncode
@@ -61,7 +71,7 @@ def get_image(filename, exp_time):
         "-r",
         "/tmp/10micron.fitsheader",
         "-x",
-        "{:d}".format(np.round(exp_time * 1000)),  # to microseconds
+        "{:d}".format(int(np.round(exp_time * 1000))),  # to microseconds
         fname,
     ]
 

focus_seq_Z1000_IXon.py

@@ -18,6 +18,7 @@ import subprocess as sp
 import numpy as np
 import socket
 import pathlib as pl
+import time
 
 
 def init_seq(seq_kwds):
@@ -30,7 +31,13 @@ def init_seq(seq_kwds):
     seq_kwds["start_idx"] = 1
     N = len(foc_files)
     if N > 0:
-        seq_kwds["start_idx"] = N
+        max = 0
+        for fname in foc_files:
+            inum = int(fname.stem.split("_")[1])
+            if inum > max:
+                max = inum
+
+        seq_kwds["start_idx"] = max + 1
 
     return 0
 
@@ -39,13 +46,28 @@ def set_focus(foc_val):
     sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     sock.connect(("ztcs.sao.ru", 4444))
 
-    sock.send("goto={:g}".format(foc_val))
-    resp = sock.recv(20)
+    bt = bytearray("goto={:g}".format(foc_val), 'utf8')
+
+    sock.send(bt)
+    resp = sock.recv(20).decode('utf8')
 
     if resp != "OK":
         sock.close()
         return 1
 
+    tp_start = time.monotonic()
+
+    while True:
+        time.sleep(0.5)
+        sock.send(b'status')
+        resp = sock.recv(20).decode('utf8')
+        if resp == 'OK':
+            break;
+
+        if (time.monotonic()-tp_start) > 30.0:
+             sock.close() # timeout!
+             return 2
+
     sock.close()
 
     return 0
@@ -55,7 +77,7 @@ def set_focus(foc_val):
 #   Assumes Andor IXon EMCCD server is listenning UNIX socket on localhost
 #
 def get_image(filename, exp_time):
-    cmd = ["ixonultra_cmdclient", "-A", "CCD", "-T", "{:g}".format(exp_time), filename]
+    cmd = ["ixonultra_cmdclient", "-A", "CCD", "-p", "1", "--hs", "0", "-T", "{:g}".format(exp_time), filename]
 
     ret = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
     return ret.returncode

focus_sequence_FLI.py

@@ -20,6 +20,9 @@ import subprocess as sp
 
 
 def set_focus(foc_val):
+    if foc_val < 0:
+        print("INVALID FLI-FOCUSER VALUE! IT MUST BE NON-NEGATIVE VALUE!")
+        return -1
     cmd = ["fli_control", "-g", str(int(foc_val))]
     ret = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
     return ret.returncode
@@ -159,8 +162,11 @@ if __name__ == "__main__":
         focus_stop = result["focus_value"] + r
 
         if args.verbose:
-            print("\testimate guess focus position in range [{:g},{:g}]".format(focus_start, focus_stop))
-
+            print(
+                "\testimate guess focus position in range [{:g},{:g}]".format(
+                    focus_start, focus_stop
+                )
+            )
 
     if np.isfinite(args.focus_step):
         result = obsutil.focussingSequence(

focus_sequence_Z1000_Ixon.py

@@ -23,7 +23,8 @@ def set_focus(foc_val):
     sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
     sock.connect(("ztcs.sao.ru", 4444))
 
-    sock.send("goto={:g}".format(foc_val))
+    print(foc_val)
+    sock.send("goto={:f}".format(foc_val))
     resp = sock.recv(20)
 
     if resp != "OK":
@@ -36,7 +37,7 @@ def set_focus(foc_val):
 
 
 def get_image(filename, exp_time):
-    cmd = ["ixonultra_cmdclient", "-A", "CCD", "-T", "{:g}".format(exp_time), filename]
+    cmd = ["ixonultra_cmdclient", "-A", "CCD", "-p", "1", "--hs", "0", "-T", "{:g}".format(exp_time), filename]
 
     ret = sp.run(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
     return ret.returncode
@@ -175,7 +176,7 @@ if __name__ == "__main__":
     if args.verbose:
         print("\tThe best focus value: {:g}".format(result["focus_value"]))
 
-    if not args.do_no_set:
+    if not args.do_not_set:
         if args.verbose:
             print("\n\tSet focus to the best value ...", end="")
             set_focus(result["focus_value"])
@@ -185,3 +186,4 @@ if __name__ == "__main__":
         print("DONE.")
 
     sys.exit(0)
+

focus_utils.py

@@ -121,11 +121,20 @@ def fitFocusCurve(
             np.inf,
         )  # parabola with minimum (2nd derivative must be positive)
 
-        if coeffs[2] < 0:
-            coeffs[2] = 0
+        if coeffs[2] < 0:  # it seems the non-robust fit failed!
+            coeffs[2] = 0  # so, guess curve is just constant!
+            coeffs[1] = 0
+            coeffs[0] = np.nanmedian(flux_rad)
+            scale = np.nanmedian(np.abs(flux_rad - coeffs[0]))
+        else:
+            nr_model = nr_res(np.asarray(focus_value))
+            scale = np.nanmedian(np.abs(flux_rad - nr_model))
+
+        # if coeffs[2] < 0:
+        #     coeffs[2] = 0
+        # nr_model = nr_res(np.asarray(focus_value))
+        # scale = np.abs(np.nanmedian(flux_rad - nr_model))
 
-        nr_model = nr_res(np.asarray(focus_value))
-        scale = np.abs(np.nanmedian(flux_rad - nr_model))
         # robust fitting
         res = least_squares(
             polyModelResid,
@@ -335,7 +344,7 @@ def focussingSequence(
         ret_val["ret_code"] = -1
         return ret_val
 
-    N = 7
+    N = 5
 
     if len(focus_range) > 2:
         if np.isclose(focus_range[2], 0):
@@ -421,7 +430,7 @@ def focussingSequence(
         # filename = "{}_{:04d}{}".format(fname, i_foc, file_ext)
         # full_filename = str(pt.Path.joinpath(dir, pt.Path(filename)))
 
-        full_filename = str(rname.with_stem("{}_{:04d}", rname.stem, i_foc))
+        full_filename = str(rname.with_stem("{}_{:04d}".format(rname.stem, i_foc)))
 
         print(log_ident, file=log_output, end="")
         print(
@@ -580,7 +589,7 @@ def getFocusCalcCmdlinePars(parser):
     parser.add_argument(
         "-o",
         "--data-curve",
-        help="filename of focussing curve data file",
+        help="filename of focussing curve ASCII data file",
         type=str,
         default=None,
     )
@@ -613,7 +622,8 @@ def getFocussingSequenceCmdlinePars(parser):
 
     parser.add_argument(
         "--foc-file",
-        help="Rootname of output focussing images. Default is 'focus.fits'.",
+        help="Rootname of output focussing images. Default is 'focus.fits'. The algorithm generates files of sequence as "
+        "'rootname_0001.rootname_ext, rootname_0002.rootname_ext ... rootname_NNNN.rootname_ext', where NNNN is an index number of acquisition.",
         type=str,
         default="focus.fits",
     )