cleanup part 2

README.md

@@ -0,0 +1,3 @@
+# Cristallina SLIC code
+
+The basic setup to control the devices at the Cristallina endstation using mostly SLIC and EPICS behind the scenes. 

cristallina.py

@@ -1,39 +1,47 @@
 #!/usr/bin/env python
 import sys
 import os
-import re
 import time
 from time import sleep
 
-from tracemalloc import start
 import numpy as np
 
-os.chdir("/sf/cristallina/applications/slic/cristallina_cleanup")
+
+# at the moment this allows us to group the subdirectories as modules easily
+# TODO: a more general way would be to have this cristallina as a installed package
+os.chdir("/sf/cristallina/applications/slic/cristallina")
 
 # setup logging
 from loguru import logger
 
-logger.remove()
-logger.add(
+
+def setup_logging():
+    logger.remove()
+    logger.add(
         sys.stderr,
         format="{time:YYYY-MM-DD at HH:mm:ss} | {level} | {message}",
         level="INFO",
-)
-logger.info("Loading started.")
+    )
+    logger.info("Loading started.")
 
-# create file handler which logs
-# TODO: better directory for log files? should not be pgroup specific so that this always works
-try:
+    # create file handler which logs
+    # TODO: better directory for log files? should not be pgroup specific so that this always works
+    try:
         logger.add(
             "/sf/cristallina/applications/slic/cristallina/log/cristallina.log",
             format="{time:YYYY-MM-DD at HH:mm:ss} | {level} | {message}",
             level="DEBUG",
         )
-except PermissionError as e:
+    except PermissionError as e:
         logger.warning("Cannot write log file.")
         logger.warning(e)
 
 
+# We setup the logging before going further so that
+# other modules can write startup messages into the log file.
+setup_logging()
+
+# TODO: this is later overwritten, probably not intended that way?
 from epics import PV
 
 from devices.alignment_laser import AlignmentLaser
@@ -55,6 +63,7 @@ from slic.devices.timing.events import CTASequencer
 from channels.bs_channels import detectors, bs_channels, camera_channels
 from channels.pv_channels import pvs
 from spreadsheet import overview
+
 # from channels_minimal import detectors_min, channels_min, pvs_min
 from devices.pp_shutter import PP_Shutter
 
@@ -88,6 +97,7 @@ OWIS = Motor("SARES30-MOBI1:MOT_6")  # small OWIS linear stage
 
 attenuator = Attenuator("SAROP31-OATA150", description="Cristallina attenuator OATA150")
 
+
 def test_attenuator():
     tfundamental = attenuator.get_transmission()
     try:
@@ -98,7 +108,9 @@ def test_attenuator():
 
 test_attenuator()
 
-front_end_attenuator = Attenuator("SARFE10-OATT053", description="Front end attenuator OATT053")
+front_end_attenuator = Attenuator(
+    "SARFE10-OATT053", description="Front end attenuator OATT053"
+)
 cta = CTASequencer("SAR-CCTA-ESC")
 
 pbps113 = IntensityMonitorPBPS(
@@ -120,13 +132,16 @@ pbps149 = IntensityMonitorPBPS(
 from beamline import undulator
 
 undulators = undulator.Undulators()
-logger.info(f"Using undulator (Aramis) offset to PSSS energy of {undulator.energy_offset} eV.")
+logger.info(
+    f"Using undulator (Aramis) offset to PSSS energy of {undulator.energy_offset} eV."
+)
 
 
 # Shutter
 shutter = PP_Shutter(
     "SARES30-LTIM01-EVR0:RearUniv0-Ena-SP", name="Cristallina pulse picker shutter"
-)  # Shutter buttton when using the pulse picker
+)  # Shutter button when using the pulse picker
+
 pulsepicker = PulsePicker(
     "SAROP31-OPPI151",
     "SARES30-LTIM01-EVR0:Pul3",
@@ -134,7 +149,9 @@ pulsepicker = PulsePicker(
 )
 
 # Alignment laser
-alaser = AlignmentLaser("SAROP31-OLAS147:MOTOR_1", name="Cristallina alignment laser OLAS147")
+alignment_laser = AlignmentLaser(
+    "SAROP31-OLAS147:MOTOR_1", name="Cristallina alignment laser OLAS147"
+)
 
 ## Slits
 from slic.devices.xoptics import slits
@@ -152,6 +169,7 @@ kbVer = KBVer("SAROP31-OKBV153", description="Cristallina vertical KB mirror")
 
 # Bernina monochromator
 from beamline.bernina_mono import BerninaMono
+
 BerninaDCM = BerninaMono("SAROP21-ODCM098")
 
 
@@ -190,6 +208,16 @@ daq = SFAcquisition(
 # There is a new EPICS buffer, so the archiver is no longer used. This makes sure we are taking PVs from the right place.
 daq.update_config_pvs()
 
+slow_daq_test = SFAcquisition(
+    instrument,
+    "p19150",
+    default_channels=bs_channels,
+    default_pvs=pvs,
+    default_detectors=detectors,
+    rate_multiplicator=100,
+)
+
+
 # daq = FakeAcquisition(instrument, pgroup)
 # daqPV = PVAcquisition(instrument, pgroup, default_channels=channels_ks) # workaround for KS not going to DB
 
@@ -208,24 +236,3 @@ gui = GUI(scan, show_goto=True, show_spec=True)
 
 logger.info(f"Running at {instrument} with pgroup {pgroup}.")
 logger.info("Loading finished.")
-
-
-
-slow_daq_test = SFAcquisition(
-    instrument,
-    "p19150",
-    default_channels=bs_channels,
-    default_pvs=pvs,
-    default_detectors=detectors,
-    rate_multiplicator=100,
-)
-
-slow_daq = SFAcquisition(
-    instrument,
-    pgroup,
-    default_channels=bs_channels,
-    default_pvs=pvs,
-    default_detectors=detectors,
-    rate_multiplicator=100,
-)
-