cgse 2024.7.0__py3-none-any.whl → 2025.0.2__py3-none-any.whl

scripts/remove_lines_between_matches.py

@@ -1,188 +0,0 @@
-"""
-This script is intended to be used for log files that contain errors or warnings that completely flood all other
-messages and therefore make it very hard to analyse the log. The script will first rename the log-file with a '.orig'
-extension and then filters out all lines between a matching start pattern and a matching end pattern.
-The filtered output is written into the original file.
-
-Example usage:
-
-    $ python remove_lines_between_matches.py ~/Desktop/general-sron.log.2023-07-14 \
-      -sp 'Executing is_connected failed' -ep '^(NotImplementedError|AttributeError)'
-
-This command will filter out all occurrences of the following two error messages:
-
-    level=ERROR ts=2023-07-14T00:00:01,065950 process=MainProcess process_id=2583919 caller=egse.protocol:595 msg="Executing is_connected failed."
-    Traceback (most recent call last):
-      File "/cgse/lib/python/egse/protocol.py", line 593, in handle_device_method
-        response = method(*args, **kwargs)
-      File "/cgse/lib/python/egse/tempcontrol/beaglebone/beaglebone.py", line 294, in is_connected
-        return all([heater.connected for heater in self.heaters])
-      File "/cgse/lib/python/egse/tempcontrol/beaglebone/beaglebone.py", line 294, in <listcomp>
-        return all([heater.connected for heater in self.heaters])
-    AttributeError: 'int' object has no attribute 'connected'
-
-and
-
-    level=ERROR ts=2023-07-14T00:00:01,285946 process=MainProcess process_id=2585980 caller=egse.protocol:595 msg="Executing is_connected failed."
-    Traceback (most recent call last):
-      File "/cgse/lib/python/egse/protocol.py", line 593, in handle_device_method
-        response = method(*args, **kwargs)
-      File "/cgse/lib/python/egse/socketdevice.py", line 124, in is_connected
-        response = self.get_idn()
-      File "/cgse/lib/python/egse/socketdevice.py", line 42, in get_idn
-        raise NotImplementedError
-    NotImplementedError
-
-"""
-
-from __future__ import annotations
-
-import argparse
-import os
-import re
-from contextlib import contextmanager
-from pathlib import Path
-
-
-@contextmanager
-def stash_file(file_name: str | Path, stash_name: str | Path = None) -> Path:
-    """
-    In the context of `stash_file` the file named `file_name` will be renamed to `stash_name`.
-    If `stash_name` is None, the suffix '.orig' will be appended to the `file_name` and used
-    as stash_name.
-
-    Upon leaving the context, the file named `file_name` will be restored to its original
-    content and file `stash_name` will be deleted.
-
-    Args:
-        file_name: the name or path of the file to stash
-        stash_name: the optional name of the stashed file
-    Returns:
-        The name of the stashed file.
-    Raises:
-        An exception is raised if the stash_name file already exists.
-    """
-
-    file_name = Path(file_name).expanduser()
-
-    if stash_name is None:
-        stash_name = Path(f"{file_name}.orig")
-    else:
-        stash_name = Path(stash_name)
-
-    # Since —on unix— the `os.rename()` function will overwrite stash_name when it exists,
-    # we already here check if the file exists.
-
-    if stash_name.exists():
-        raise EnvironmentError(f"{stash_name} already exists, please remove/rename it before proceeding.")
-
-    try:
-        os.rename(file_name, stash_name)
-    except FileNotFoundError as exc:
-        raise EnvironmentError(f"No such file: {file_name}") from exc
-    except OSError as exc:
-        raise EnvironmentError(f"Please remove {stash_name}") from exc
-
-    try:
-        yield stash_name
-    finally:
-        os.replace(stash_name, file_name)
-
-
-def rename_file(name: str | Path, new_name: str | Path) -> Path:
-    """
-    Rename a file.
-
-    This will also work if the new_name is in a different folder as the original name.
-
-    Args:
-        name: the name of the original file to be stashed
-        new_name: the name to use for the stashed file
-
-    Returns:
-        The name of the stashed file.
-    Raises:
-        An exception is raised if the stash_name file already exists.
-
-    """
-    name = Path(name).expanduser()
-    new_name = Path(new_name).expanduser()
-
-    # Since —on unix— the `os.rename()` function will overwrite stash_name when it exists,
-    # we already here check if the file exists.
-
-    if new_name.exists():
-        raise EnvironmentError(f"{new_name} already exists, please remove/rename it before proceeding.")
-
-    try:
-        os.rename(name, new_name)
-    except FileNotFoundError as exc:
-        raise EnvironmentError(f"No such file: {name}") from exc
-    except OSError as exc:
-        raise EnvironmentError(f"{new_name} already exists, please remove/rename it before proceeding.") from exc
-
-    return new_name
-
-
-def main():
-
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--start_pattern", "-sp", required=True)
-    parser.add_argument("--end_pattern", "-ep", required=True)
-    parser.add_argument("path")
-
-    args = parser.parse_args()
-
-    moved_fn = rename_file(args.path, f"{args.path}.orig")
-
-    start_marker = args.start_pattern
-    end_marker = args.end_pattern
-
-    with open(moved_fn, mode='r') as in_fd, open(args.path, mode='w') as out_fd:
-        ignore_lines = False
-        last_line_empty = False
-        for line in in_fd:
-            if re.search(start_marker, line):
-                ignore_lines = True
-            elif re.search(end_marker, line):
-                ignore_lines = False
-            elif not ignore_lines:
-                if line.strip() == '':
-                    if not last_line_empty:
-                        last_line_empty = True
-                        out_fd.write(line)
-                else:
-                    out_fd.write(line)
-                    last_line_empty = False
-
-
-def test_stash_file():
-
-    fn = Path("~/Desktop/xxx.txt").expanduser()
-    assert fn.exists()
-
-    with stash_file(fn) as sfn:
-        stash_name = sfn
-        assert stash_name.exists()
-        assert not fn.exists()
-
-    assert fn.exists()
-    assert not stash_name.exists()
-
-
-def test_rename_file():
-
-    fn = Path("~/Desktop/xxx.txt").expanduser()
-
-    assert fn.exists()
-
-    moved_fn = rename_file(fn, "~/tmp/yyy.out")
-
-    assert not fn.exists()
-    assert moved_fn.exists()
-
-
-if __name__ == '__main__':
-    main()
-    # test_stash_file()
-    # test_move_file()

scripts/sron/commanding/control_heaters.py

@@ -1,44 +0,0 @@
-#!/usr/bin/env python3
-
-import logging
-import time
-
-from argparse import ArgumentParser
-
-from egse.tempcontrol.beaglebone.beaglebone import BeagleboneProxy
-
-log = logging.getLogger(__name__)
-logging.basicConfig()
-
-parser = ArgumentParser()
-parser.add_argument('device', type=int, help='beaglebone device index [0, 1]')
-parser.add_argument('channel', type=int, help='beaglebone pwm channel [0, 3]')
-parser.add_argument('setpoint', type=int, help='pwm duty cycle in %%')
-args = parser.parse_args()
-
-assert args.device in [0, 1, 2, 3], 'device index must be in [0 - 3]'
-assert args.channel in [0, 1, 2, 3], 'pwm channel must be in [0 - 3]'
-assert args.setpoint in range(0, 101), 'pwm duty cycle must be in [0 - 100]'
-
-try:
-    beaglebone = BeagleboneProxy()
-except Exception as e:
-    log.error(f'could not connect to beaglebone control server ({e})')
-else:
-    log.info('connected to beaglebone control server')
-
-try:
-    beaglebone.set_period(args.device, args.channel, 10000)
-    beaglebone.set_duty_cycle(args.device, args.channel, (args.setpoint * 100))
-    if args.setpoint == 0:
-        beaglebone.set_enable(args.device, args.channel, False)
-    else:
-        beaglebone.set_enable(args.device, args.channel, True)
-except Exception as e:
-    log.error(f'could not set duty cycle ({e})')
-
-while True:
-    time.sleep(1)
-    print(beaglebone.get_voltage(args.device, args.channel), 'V')
-    print(beaglebone.get_current(args.device, args.channel), 'A')
-    print(beaglebone.get_power(args.device, args.channel), 'W')

scripts/sron/commanding/pumpdown.py

@@ -1,46 +0,0 @@
-#!/usr/bin/env python3
-
-import logging
-from time import sleep
-
-from egse.vacuum.instrutech.igm402 import Igm402Proxy
-from egse.vacuum.pfeiffer.tc400 import Tc400Proxy
-from egse.vacuum.pfeiffer.acp40 import Acp40Proxy
-
-log = logging.getLogger(__name__)
-logging.basicConfig()
-
-igm402 = Igm402Proxy()
-tc400 = Tc400Proxy()
-acp40 = Acp40Proxy()
-
-# TODO: check vessel door interlock
-# TODO: open gate valve
-
-log.info('Starting ACP40')
-acp40.set_enable(enable=True)
-
-log.info('Waiting for pressure to reach 6E-0 mbar...')
-while (igm402.get_cgn_pressure(index=1) > 6E-0):
-    sleep(1)
-log.info('Starting TC400')
-tc400.set_pumpingstation(enable=True)
-tc400.set_motorpump(enable=True)
-
-log.info('Waiting for pressure to reach 1.1E-3 mbar...')
-while (igm402.get_cgn_pressure(index=1) > 1.1E-3):
-    last_error = tc400.get_last_error()
-    if last_error != 0:
-        log.error(f'TC400 error: {last_error}')
-        tc400.set_pumpingstation(enable=False)
-        exit()
-    sleep(1)
-
-# log.info('Turn on ionization gauge')
-igm402.set_filament_enable(enable=True)
-
-log.info('Waiting for pressure to reach 1E-5 mbar...')
-while (igm402.get_ion_gauge_pressure() > 1E-5):
-    sleep(1)
-
-log.info('Ready for cooling')

scripts/sron/commanding/set_pid_setpoint.py

@@ -1,19 +0,0 @@
-#!/usr/bin/env python3
-
-from argparse import ArgumentParser
-from egse.tempcontrol.spid.spid import PidProxy
-
-parser = ArgumentParser()
-parser.add_argument('channel', type=int, help='channel index')
-parser.add_argument('setpoint', type=float, help='temperature setpoint')
-parser.add_argument('enable', type=bool, help="Enable controller")
-
-args = parser.parse_args()
-
-p = PidProxy()
-
-if args.enable:
-    p.set_temperature(args.channel, args.setpoint)
-    p.enable(args.channel)
-else:
-    p.disable(args.channel)

scripts/sron/commanding/shutdown_bbb_heaters.py

@@ -1,10 +0,0 @@
-#!/usr/bin/env python3
-
-from egse.tempcontrol.beaglebone.beaglebone import BeagleboneProxy
-
-bbb = BeagleboneProxy()
-
-for device in range(4):
-    for channel in range(4):
-        bbb.set_enable(device, channel, False)
-        #print(bbb.get_current(device, channel))

scripts/sron/commanding/shutdown_pumps.py

@@ -1,33 +0,0 @@
-#!/usr/bin/env python3
-
-import logging
-from time import sleep
-
-from egse.vacuum.instrutech.igm402 import Igm402Proxy
-from egse.vacuum.pfeiffer.tc400 import Tc400Proxy
-from egse.vacuum.pfeiffer.acp40 import Acp40Proxy
-
-log = logging.getLogger(__name__)
-logging.basicConfig()
-
-igm402 = Igm402Proxy()
-tc400 = Tc400Proxy()
-acp40 = Acp40Proxy()
-
-# TODO: turn of vacscan filament
-# TODO: close gate valve
-
-log.info('Turn of IGM402 filament')
-igm402.set_filament_enable(enable=False)
-
-log.info('Shut down TC400')
-tc400.set_pumpingstation(enable=False)
-
-log.info('Waiting for tc400 to reach 50 Hz...')
-while (tc400.get_active_speed() > 50):
-    sleep(1)
-
-log.info('Shut down ACP40')
-acp40.set_enable(enable=False)
-
-log.info('Done')

scripts/sron/correct_mgse_coordinates_brigand_chimay.py

@@ -1,272 +0,0 @@
-#!/usr/bin/env python3
-import argparse
-import os
-import shutil
-import logging
-
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-
-from datetime import datetime
-from dateutil.rrule import rrule, DAILY
-
-from scripts.sron.gimbal_conversions import gimbal_rotations_to_fov_angles
-from egse.obsid import obsid_from_storage
-from egse.config import find_file
-
-logger = logging.getLogger(__name__)
-
-FOV_ORIGIN = 'FOV'
-ENSEMBLE_ORIGIN = 'ENSEMBLE'
-
-
-def correct_brigand_chimay(data_dir: str = None):
-    data_dir = data_dir or os.environ['PLATO_DATA_STORAGE_LOCATION']
-
-    correct_obsid_range(308, 382, "brigand", data_dir)
-    correct_obsid_range(383, 391, "arthureddington", data_dir)
-    correct_obsid_range(392, 688, "brigand", data_dir)
-    correct_obsid_range(831, 1109, "chimay", data_dir)
-
-    correct_od_range(20230629, 20231020, data_dir)
-
-
-def correct_obsid_range(first_obsid: int, last_obsid: int, camera_name: str, data_dir: str):
-    """
-     Recompute the FOV housekeeping for the obsid range.
-
-     This function does the following:
-
-        * Make a copy of the original FOV files (incl. "old" in the filename)
-        * In the original files:
-            - Recompute all actual and commanded positions based on ENSEMBLE HK
-
-     Args:
-         - first_obsid: First obsid.
-         - last_obsid: Last obsid.
-         - data_dir: Full path to the directory in which the data resides.  This is the
-         folder with sub-folders /obs and /daily, in which the FOV and ENSEMBLE HK files
-         are stored.
-    """
-    for obsid in range(first_obsid, last_obsid+1):
-        correct_obsid(obsid, camera_name, data_dir)
-
-
-def correct_obsid(obsid: int, camera_name: str, data_dir: str):
-    """
-     Recompute the FOV housekeeping for the given obsid.
-
-     This function does the following:
-
-        * Make a copy of the original FOV file (incl. "old" in the filename)
-        * In the original file:
-            - Recompute all actual and commanded positions based on ENSEMBLE HK
-
-     Args:
-         - obsid: Observation identifier.
-         - data_dir: Full path to the directory in which the data resides.  This is the
-         folder with sub-folders /obs and /daily, in which the FOV and ENSEMBLE HK files
-         are stored.
-    """
-
-    stored_obsid = obsid_from_storage(obsid,
-                                      data_dir=data_dir,
-                                      site_id="SRON",
-                                      camera_name=camera_name)
-
-    fov_pattern = f"{stored_obsid}_{FOV_ORIGIN}_*.csv"
-    gimbal_pattern = f"{stored_obsid}_{ENSEMBLE_ORIGIN}_*.csv"
-
-    fov_hk_filename = find_file(fov_pattern, root=f"{data_dir}/obs/{stored_obsid}")
-    gimbal_hk_filename = find_file(gimbal_pattern, root=f"{data_dir}/obs/{stored_obsid}")
-
-    if fov_hk_filename is None:
-        logger.warning(f"No FOV HK available for OBSID {stored_obsid}")
-        return
-
-    if gimbal_hk_filename is None:
-        logger.warning(f"No ENSEMBLE HK available for OBSID {stored_obsid}")
-        return
-
-    correct_valid_file(str(fov_hk_filename), str(gimbal_hk_filename))
-
-
-def correct_od_range(first_od: int, last_od: int, data_dir: str):
-    """
-     Recompute the FOV housekeeping for the OD range.
-
-     This function does the following:
-
-        * Make a copy of the original FOV files (incl. "old" in the filename)
-        * In the original files:
-            - Recompute all actual and commanded positions based on ENSEMBLE HK.
-
-     Args:
-         - first_od: First observing day [yyyymmdd].
-         - last_od: Last observing day [yyyymmdd].
-         - data_dir: Full path to the directory in which the data resides.  This is the
-         folder with sub-folders /obs and /daily, in which the FOV and ENSEMBLE HK files
-         are stored.
-    """
-    start = datetime.strptime(str(first_od), "%Y%m%d")
-    end = datetime.strptime(str(last_od), "%Y%m%d")
-
-    for dt in rrule(DAILY, dtstart=start, until=end):
-        correct_od(dt.strftime("%Y%m%d"), data_dir)
-
-
-def correct_od(od: int, data_dir: str):
-    """
-     Recompute the FOV housekeeping for the given OD.
-
-     This function does the following:
-
-        * Make a copy of the original FOV files (incl. "old" in the filename)
-        * In the original files:
-            - Recompute all actual and commanded positions based on ENSEMBLE HK.
-
-     Args:
-         - od: Observing day [yyyymmdd].
-         - data_dir: Full path to the directory in which the data resides.  This is the
-         folder with sub-folders /obs and /daily, in which the FOV and ENSEMBLE HK files
-         are stored.
-    """
-    fov_pattern = f"{od}_SRON_{FOV_ORIGIN}.csv"
-    gimbal_pattern = f"{od}_SRON_{ENSEMBLE_ORIGIN}.csv"
-
-    fov_hk_filename = find_file(fov_pattern, root=f"{data_dir}/daily/{od}")
-    gimbal_hk_filename = find_file(gimbal_pattern, root=f"{data_dir}/daily/{od}")
-
-    if fov_hk_filename is None:
-        logger.warning(f"No FOV HK file '{fov_pattern}' available for OD {od}")
-        return
-
-    if gimbal_hk_filename is None:
-        logger.warning(f"No ENSEMBLE HK file '{gimbal_pattern}' available for OD {od}")
-        return
-
-    correct_valid_file(str(fov_hk_filename), str(gimbal_hk_filename))
-
-
-def add_angles_row(angles_dict, timestamp, act_theta, act_phi, cmd_theta=np.nan,
-                   cmd_phi=np.nan):
-    """ Appends a row to the angles dictionary
-
-    Args:
-        - angles_dict: dictionary representing a pandas dataframe
-        - timestamp: timestamp from the gimbal housekeepng file
-        - act_theta: recomputed actual theta angle
-        - act_phi: recomputed actual phi angle
-        - cmd_theta: recomputed commanded theta angle
-        - cmd_phi: recomputed commanded phi angle
-
-    """
-    angles_dict['timestamp'].append(timestamp)
-    angles_dict['FOV_ACT_THETA'].append(act_theta)
-    angles_dict['FOV_ACT_PHI'].append(act_phi)
-    angles_dict['FOV_CMD_THETA'].append(cmd_theta)
-    angles_dict['FOV_CMD_PHI'].append(cmd_phi)
-
-
-def correct_valid_file(fov_filename: str, gimbal_filename: str, plot: bool = False):
-    """ Recompute the theta, phi values in the FOV HK file with the given filename.
-
-    This function does the following:
-
-        * Make a copy of the original file (incl. "old" in the filename).
-        * Iterate over all rows in ENSEMBLE housekeeping
-            - For each row, recompute the actual theta and phi.
-            - When the gimbal is not moving, and the previous commanded position !=
-            current commanded position, recompute the commanded theta and phi.
-
-    Args:
-        - fov_filename: Filename of the original FOV HK file that needs to be corrected.
-        - gimbal_filename: Filename of the ensemble HK file with the valid X, Y
-        coordinates.
-    """
-    # Make a copy of the original file (incl. "old" in the filename) in the same folder
-    logger.info(f"Now correcting: {fov_filename}")
-
-    copy_fov_filename = f"{fov_filename.split('.')[0]}_old.csv"
-    if not os.path.isfile(copy_fov_filename):
-        shutil.copyfile(fov_filename, copy_fov_filename)
-
-    # Iterate over all rows in the FOV HK
-    # angles_df = pd.read_csv(fov_filename)
-    angles_dict = {
-        'timestamp': [],
-        'FOV_ACT_THETA': [],
-        'FOV_ACT_PHI': [],
-        'FOV_CMD_THETA': [],
-        'FOV_CMD_PHI': []
-    }
-
-    coordinates_df = pd.read_csv(gimbal_filename)
-    len_coordinates_ds = len(coordinates_df)
-
-    is_moving = False
-
-    previous_commanded_position = (np.nan, np.nan)
-
-    for i, row in coordinates_df.iterrows():
-        print(f"Now correcting row {i+1:06}/{len_coordinates_ds:06}\r", end="")
-
-        # Extract timestamp, status, actual positions and commanded positions
-        timestamp = row['timestamp']
-
-        status_plane = row['GSRON_ENSEMBLE_STATUS_PLANE']
-
-        act_x, act_y = (row['GSRON_ENSEMBLE_ACT_POS_X'],
-                        row['GSRON_ENSEMBLE_ACT_POS_Y'])
-
-        cmd_x, cmd_y = (row['GSRON_ENSEMBLE_CMD_POS_X'],
-                        row['GSRON_ENSEMBLE_CMD_POS_Y'])
-
-        # Recompute and save commanded positions when gimbal stops moving
-        # Also compare commanded position vs. previous commanded position to prevent
-        # false positives
-        if (cmd_x, cmd_y) != previous_commanded_position and not status_plane & 0x1:
-            if is_moving is True:
-                is_moving = False
-                # Recompute and save commanded position
-                cmd_theta, cmd_phi = gimbal_rotations_to_fov_angles(cmd_x, cmd_y)
-                add_angles_row(angles_dict, timestamp, np.nan, np.nan, cmd_theta, cmd_phi)
-            previous_commanded_position = (cmd_x, cmd_y)
-        else:
-            is_moving = True
-
-        # Recompute and save actual positions for each row
-        act_theta, act_phi = gimbal_rotations_to_fov_angles(act_x, act_y)
-        add_angles_row(angles_dict, timestamp, act_theta, act_phi)
-
-    print("")
-    angles_df = pd.DataFrame(angles_dict)
-    angles_df.to_csv(fov_filename, index=False)
-
-    if plot:
-        angles_df.plot(x='timestamp', y=['FOV_ACT_THETA',
-                                             'FOV_CMD_THETA',
-                                             'FOV_ACT_PHI',
-                                             'FOV_CMD_PHI'], style=['-', 'o', '-', 'o'])
-        plt.show()
-
-
-def main():
-    parser = argparse.ArgumentParser(description="CLI tool for correcting FOV "
-                                                 "housekeeping - PLATO-INAF-PL-NCR-0013")
-    parser.add_argument('data_dir', type=str,
-                        help='Full path to the directory in which the data resides.  '
-                             'This is the folder with sub-folders /obs and /daily, '
-                             'in which the N-FEE HK files are stored.  '
-                             'Default is the content of the '
-                             'PLATO_DATA_STORAGE_LOCATION environment variable.')
-
-    args = parser.parse_args()
-
-    correct_brigand_chimay(args.data_dir)
-
-
-if __name__ == "__main__":
-    main()
-