Merge pull request #66 from pcdshub/60-add-cctbx-class

60 add cctbx class

.gitignore

@@ -3,6 +3,9 @@ logs
 # Ignore generated database file
 mfx/db.txt
 
+# Ignore changed presets
+presets/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

mfx/bash_utilities.py

@@ -1,78 +1,121 @@
-def xfel_gui():
-    import subprocess
-    import logging
-    from mfx.macros import get_exp
-
-    logging.info("Checking xfel gui phil File")
-    cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_old.phil", "r", encoding="UTF-8")
-    setting_lines = cctbx_settings.readlines()
-    change = False
-
-    if setting_lines[10] != f'name = "{get_exp()}"':
-        logging.warning(f"Changing experiment to current: {get_exp()}")
-        setting_lines[10] = f'  name = "{get_exp()}"\n'
-        change = True
-
-    if setting_lines[11] != f'user = "{get_exp()}"':
-        logging.warning(f"Changing experiment to current: {get_exp()}")
-        setting_lines[11] = f'  user = "{get_exp()}"\n'
-        change = True
-
-    if change:
-        cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings.phil", "w", encoding="UTF-8")
-        cctbx_settings.writelines(setting_lines)
-        cctbx_settings.close
-        cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_old.phil", "w", encoding="UTF-8")
-        cctbx_settings.writelines(setting_lines)
-        cctbx_settings.close
-
-    subprocess.Popen(
-        [". /reg/g/cctbx/brewster/working/build/conda_setpaths.sh;cctbx.xfel &"],
-        shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
+class bs:
+    def xfel_gui(self):
+        import subprocess
+        import logging
+        from mfx.macros import get_exp
+
+        logging.info("Checking xfel gui phil File")
+        cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_old.phil", "r", encoding="UTF-8")
+        setting_lines = cctbx_settings.readlines()
+        change = False
+
+        if setting_lines[10] != f'name = "{get_exp()}"':
+            logging.warning(f"Changing experiment to current: {get_exp()}")
+            setting_lines[10] = f'  name = "{get_exp()}"\n'
+            change = True
+
+        if setting_lines[11] != f'user = "{get_exp()}"':
+            logging.warning(f"Changing experiment to current: {get_exp()}")
+            setting_lines[11] = f'  user = "{get_exp()}"\n'
+            change = True
+
+        if change:
+            cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings.phil", "w", encoding="UTF-8")
+            cctbx_settings.writelines(setting_lines)
+            cctbx_settings.close
+            cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_old.phil", "w", encoding="UTF-8")
+            cctbx_settings.writelines(setting_lines)
+            cctbx_settings.close
+
+        subprocess.Popen(
+            [". /reg/g/cctbx/brewster/working/build/conda_setpaths.sh;cctbx.xfel &"],
+            shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
+
+
+    def takepeds(self):
+        import os
+        import logging
+        logging.info("Taking Pedestals")
+        os.system(f"/reg/g/pcds/engineering_tools/latest-released/scripts/takepeds")
+
+
+    def makepeds(self, username, run_number=None):
+        import os
+        import logging
+        from mfx.db import daq
+        from mfx.macros import get_exp
+        logging.info("Making Pedestals")
+        if run_number is None:
+            run_number = daq.run_number()
+        username = str(username)
+        run_number = str(int(run_number))
+        os.system(f"ssh -Y {username}@s3dflogin ssh -Y psana /sdf/group/lcls/ds/tools/engineering_tools/engineering_tools/scripts/makepeds_psana --queue milano --run {run_number} --experiment {get_exp()}")
+
+
+    def awr(self, hutch='mfx'):
+        import os
+        import logging
+        logging.info(f"{hutch} Beamline Check")
+        os.system(f"/cds/home/opr/mfxopr/bin/awr {hutch}")
+
+
+    def restartdaq(self):
+        import subprocess
+        import logging
+        logging.info("Restarting the DAQ")
+        subprocess.Popen(
+            ["/reg/g/pcds/engineering_tools/latest-released/scripts/restartdaq -w"],
+            shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
+
 
+    def cameras(self, time=12):   
+        import subprocess
+        import logging
+        logging.info("Opening Cam Viewer")
+        subprocess.Popen(
+            [f"/reg/g/pcds/engineering_tools/latest-released/scripts/camViewer -w {time}"],
+            shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
+
+
+    def camera_list(self):
+        import re   
+        import logging
+        logging.info("Opening Camera List")
+        camlist = open("/reg/g/pcds/pyps/config/mfx/camviewer.cfg", "r", encoding="UTF-8")
+        cam_list = camlist.readlines()
+        avail_cams = [cam for cam in cam_list if cam.startswith('GE')]
+        self.camera_names = [['camera_name', 'camera_pv']]
+        print("Available Cameras")
+        for cam in avail_cams:
+            cam = re.split(';|,', cam)
+            self.camera_names.append([cam[4].strip(),cam[2]])
+            print(f"Camera {cam[4].strip()} ....  {cam[2]}")
+
+
+    def focus_scan(self, camera):
+        import os
+        import sys
+        import logging
+        logging.info(
+            "Preparing for Focus Scan\n"
+            "Please check the following\n"
+            "One of the following cameras is selected\n\n")
+        self.camera_list()
+        logging.info(
+            "\nCamera orientation set to none\n"
+            "Slits are open\n"
+            "Blue crosshair in upper left corner\n"
+            "Red crosshair in bottom right corner\n")
+
+        input("Press Enter to continue...")
+
+        if camera not in [pv[1] for pv in self.camera_names]:
+            logging.info("Desired Camera not in List. Software will exit.")
+            sys.exit()
+
+        logging.info("Checking Focus Scan Plot")
+        os.system(f"/cds/home/opr/mfxopr/bin/focus_scan {camera} -p")
+        input("Press Enter to continue...")
 
-def takepeds():
-    import os
-    import logging
-    logging.info("Taking Pedestals")
-    os.system(f"/reg/g/pcds/engineering_tools/latest-released/scripts/takepeds")
-
-
-def makepeds(username, run_number=None):
-    import os
-    import logging
-    from mfx.db import daq
-    from mfx.macros import get_exp
-    logging.info("Making Pedestals")
-    if run_number is None:
-        run_number = daq.run_number()
-    username = str(username)
-    run_number = str(int(run_number))
-    os.system(f"ssh -Y {username}@s3dflogin ssh -Y psana /sdf/group/lcls/ds/tools/engineering_tools/engineering_tools/scripts/makepeds_psana --queue milano --run {run_number} --experiment {get_exp()}")
-
-
-def awr(hutch='mfx'):
-    import os
-    import logging
-    logging.info(f"{hutch} Beamline Check")
-    os.system(f"/cds/home/opr/mfxopr/bin/awr {hutch}")
-
-
-def restartdaq():
-    import subprocess
-    import logging
-    logging.info("Restarting the DAQ")
-    subprocess.Popen(
-        ["/reg/g/pcds/engineering_tools/latest-released/scripts/restartdaq -w"],
-        shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
-    #os.system("/reg/g/pcds/engineering_tools/latest-released/scripts/restartdaq -w")
-
-
-def cameras(time=12):   
-    import subprocess
-    import logging
-    logging.info("Opening Cam Viewer")
-    subprocess.Popen(
-        [f"/reg/g/pcds/engineering_tools/latest-released/scripts/camViewer -w {time}"],
-        shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
-    #os.system(f"/reg/g/pcds/engineering_tools/latest-released/scripts/camViewer -w {time}")
+        logging.info("Running Focus Scan")
+        os.system(f"/cds/home/opr/mfxopr/bin/focus_scan {camera} -s")

mfx/beamline.py

@@ -12,6 +12,8 @@
     from pcdsdevices.sequencer import EventSequencer
     sequencer = EventSequencer('ECS:SYS0:7', name='mfx_sequencer')
     mfx_sequencer = sequencer
+    sequencer2 = EventSequencer('ECS:SYS0:12', name='mfx_sequencer_spare')
+    mfx_sequencer_spare = sequencer2
 
 with safe_load('rayonix utils'):
     from mfx.rayonix import Rayonix
@@ -37,10 +39,12 @@
 
 with safe_load('macros'):
     from mfx.macros import *
+
+with safe_load('MFX_Timing'):
+    from mfx.mfx_timing import *
     mfx_timing = MFX_Timing(sequencer)
 
 with safe_load('Droplet_on_Demand'):
-    # from mfx.mfxDOD import *
     from mfx.mfx_dod import *
 
 with safe_load('delay_scan'):
@@ -73,6 +77,7 @@
 
 with safe_load('bash_utilities'):
     from mfx.bash_utilities import *
+    bs = bs()
 
 with safe_load('cctbx'):
     from mfx.cctbx import *

mfx/cctbx.py

@@ -1,81 +1,50 @@
 class cctbx:
     def __init__(self):
         from mfx.macros import get_exp
-        self.settings = "~/.cctbx.xfe/settings_old.phil"
         self.experiment = str(get_exp())
 
 
-    def check_settings(self, user):
+    def xfel_gui(self, user):
         import logging
         import subprocess
-        exp = self.experiment
-        logging.info("Checking xfel gui phil File")
-        cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_s3df.phil", "r", encoding="UTF-8")
-        setting_lines = cctbx_settings.readlines()
-        change = False
-        if setting_lines[4] != f'experiment =  "{exp}"':
-            logging.warning(f"Changing experiment to current: {exp}")
-            change = True
-            settings = f'''\
-facility {{
-  name = *lcls standalone
-  lcls {{
-    experiment = "{exp}"
-    web {{
-      location = "S3DF"
-    }}
-  }}
-}}
-output_folder = "/sdf/data/lcls/ds/mfx/{exp}/results/common/results"
-mp {{
-  method = local lsf sge pbs *slurm shifter htcondor custom
-  nnodes_index = 2
-  nnodes_scale = 1
-  nnodes_merge = 1
-  nproc_per_node = 120
-  queue = "milano"
-  extra_options = " --account=lcls:{exp} --reservation=lcls:onshift"
-  env_script = "/sdf/group/lcls/ds/tools/cctbx/build/conda_setpaths.sh"
-  phenix_script = "/sdf/group/lcls/ds/tools/cctbx/phenix/phenix-1.20.1-4487/phenix_env.sh"
-}}
-experiment_tag = "common"
-db {{
-  host = "172.24.5.182"
-  name = "{exp}"
-  user = "{exp}"
-}}\
-'''
-        if change:
-            cctbx_settings = open("/cds/home/opr/mfxopr/.cctbx.xfel/settings_s3df.phil", "w", encoding="UTF-8")
-            cctbx_settings.writelines(settings)
-            cctbx_settings.close
+        self.settings = f"/sdf/home/{user[0]}/{user}/.cctbx.xfel/settings.phil"
+        self.cctbx_dir = f"/sdf/home/{user[0]}/{user}"
 
-            subprocess.Popen(
-                [f"rsync -avze ssh ~/.cctbx.xfel/settings_s3df.phil {user}@s3dflogin:~/.cctbx.xfel/settings_old.phil"],
-                shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
+        proc = [
+            f"ssh -YAC {user}@s3dflogin "
+            f"/sdf/home/d/djr/scripts/cctbx_step1.sh {user} {self.experiment}"
+            ]
 
+        logging.info(proc)
+
+        subprocess.Popen(
+            proc, shell=True, 
+            stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
 
-    def xfel_gui(self, user):
+
+    def notch_check(self, user, runs=[]):
         import logging
         import subprocess
-        import os
-
-        #cctbx_dir = 
-        if not os.path.exists(out_result):
-            os.makedirs(out_result)
+        import sys
+        if len(runs) > 0:
+            run_list = []
+            for run in runs:
+                run_list.append(f'{experiment}:{run}')
+            logging.info(f'Selected runs: {run_list}')
+            runlist = ' '
+            runlist = runlist.join(run_list)
+            logging.info(f'Selected runs: {runlist}')
+        else:
+            logging.warning(f'No selected runs. Program will exit.')
+            sys.exit()
 
         proc = [
-            f"ssh -YAC mfxopr@daq-mfx-mon0{str(node)} "
-            f"/cds/group/pcds/pyps/apps/hutch-python/mfx/scripts/"
-            f"detector_image.sh {experiment} {str(det)} {str(calibdir)} {str(ave)}"
+            f'ssh -YAC {user}@s3dflogin '
+            f'/sdf/home/d/djr/scripts/cctbx_notch_check.sh "{self.runlist}"'
             ]
-        
+
         logging.info(proc)
 
         subprocess.Popen(
             proc, shell=True, 
             stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
-
-        subprocess.Popen(
-            [". /reg/g/cctbx/brewster/working/build/conda_setpaths.sh;cctbx.xfel &"],
-            shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)