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

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This commit is contained in:
Timur A. Fatkhullin
2024-10-11 17:06:08 +03:00
parent 2113f87eed
commit b7750ee029
4 changed files with 89 additions and 24 deletions
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39
focus_app.py
View File

@@ -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,
get_image,
init_seq_func,
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,
get_image,
init_seq_func,
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,
get_image,
init_seq_func,
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:

22
focus_seq_FLI.py
View File

@@ -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)

18
focus_seq_Z1000_IXon.py
View File

@@ -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)

34
focus_utils.py
View File

@@ -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
fname = rname.stem
file_ext = rname.suffix
if file_ext == "":
file_ext = ".fit"
# dir = rname.parent
# fname = rname.stem
# file_ext = rname.suffix
# if file_ext == "":
# 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)
full_filename = str(pt.Path.joinpath(dir, pt.Path(filename)))
# 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))
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: