doc/changelog.rst

@@ -11,6 +11,8 @@ unreleased
     - fix :issue:`46` with a change in dask groupby mean behavior :mr:`174`
     - fix :issue:`47` SLURM script not using the correct kernel :mr:`176`
     - fix :issue:`51` make sure that BAM units are in ps :mr:`183`
+    - fix :issue:`50` and :issue:`54` relating to package dependencies
+		- fix :issue:`57` adds target mono energy mnemonic
 
 - **Improvements**
 

doc/maintainers.rst

@@ -70,7 +70,7 @@ Installing additional packages
 In order to install additional packages in a Toolbox environment, one should
 run the following commands:
 
-.. code::shell
+.. code:: shell
 
     cd <PROPOSAL_PATH>/usr/Software/
     source envs/toolbox_<IDENTIFIER>/bin/activate

doc/scripts/bin_dssc_module_job.sh

@@ -25,7 +25,7 @@ done
 # Load xfel environment
 source /etc/profile.d/modules.sh
 module load exfel
-module load exfel_anaconda3/1.1
+module load exfel_anaconda3
 
 echo processing run $RUN
 PDIR=$(find-proposal $PROPOSAL)

doc/scripts/boz_parameters_job.sh

@@ -30,7 +30,7 @@ done
 # Load xfel environment
 source /etc/profile.d/modules.sh
 module load exfel
-module load exfel_anaconda3/1.1
+module load exfel_anaconda3
 
 echo processing run $RUN
 PDIR=$(find-proposal $PROPOSAL)

doc/scripts/format_data.sh

@@ -8,11 +8,11 @@ if [ -d $RUN_DIR ]
     then 
         echo creating formatted .h5 file for run $RUN_NR in $RUN_DIR
 #         module load exfel
-#         module load exfel_anaconda3/1.1
+#         module load exfel_anaconda3
         python format_data.py --run-number $RUN_NR --run-folder $RUN_DIR
         #chgrp -R 60002711-part $RUN_DIR
         chmod -R 777 $RUN_DIR
     else
         echo run folder $RUN_DIR does not exist
         echo please provide a valid run number
-fi
+fi
\ No newline at end of file

doc/scripts/start_job_single.sh

@@ -11,7 +11,7 @@ RUNTYPE=$3
 
 source /etc/profile.d/modules.sh
 module load exfel
-module load exfel_anaconda3/1.1
+module load exfel_anaconda3
 
 echo processing modules $MODULES of run $RUN
 python process_data_201007_23h.py --run-number $RUN --module ${MODULES} --runtype $RUNTYPE

doc/scripts/start_processing_all.sh

@@ -8,7 +8,7 @@ if [ $RUN ] && [ $RUNTYPE ]
         echo processing run $RUN
         source /etc/profile.d/modules.sh
         module load exfel
-        module load exfel_anaconda3/1.1
+        module load exfel_anaconda3
         
         sbatch ./start_job_single.sh $RUN '0 1 2 3' $RUNTYPE
         sbatch ./start_job_single.sh $RUN '4 5 6 7' $RUNTYPE

setup.py

@@ -12,8 +12,9 @@ basic_analysis_reqs = ['numpy', 'scipy',]  # and is readily available in Karabo
 advanced_analysis_reqs = [
     'pandas', 'imageio', 'xarray>=0.13.0', 'psutil', 'h5py', 'h5netcdf',]
 interactive_reqs = ['ipykernel', 'matplotlib', 'tqdm',]
-maxwell_reqs = ['joblib', 'papermill', 'dask',
-                'extra_data', 'euxfel_bunch_pattern>=0.6']
+maxwell_reqs = ['joblib', 'papermill', 'dask[diagnostics]',
+                'extra_data', 'extra_geom', 'euxfel_bunch_pattern>=0.6',
+                'pyFAI',]
 docs_reqs = ['sphinx', 'nbsphinx']
 
 setup(name='toolbox_scs',

src/toolbox_scs/constants.py

@@ -62,7 +62,9 @@ mnemonics = {
     "nrj": ({'source': 'SA3_XTD10_MONO/MDL/PHOTON_ENERGY',
              'key': 'actualEnergy.value',
              'dim': None},),
-
+    "nrj_target": ({'source': 'SA3_XTD10_MONO/MDL/PHOTON_ENERGY',
+                    'key': 'targetEnergy.value',
+                    'dim': None},),
     "M2BEND": ({'source': 'SA3_XTD10_MIRR-2/MOTOR/BENDER',
                 'key': 'actualPosition.value',
                 'dim': None},),
@@ -371,6 +373,9 @@ mnemonics = {
     "PP800_HalfWP": ({'source': 'SCS_ILH_LAS/MOTOR/ROT8WP1',
                       'key': 'actualPosition.value',
                       'dim': None},),
+    "PP800_HWP_POWER": ({'source': 'SCS_ILH_LAS/MDL/WAVEPLATE_PP800',
+                         'key': 'actualPosition.value',
+                         'dim': None},),   
     "PP800_FocusLens": ({'source': 'SCS_ILH_LAS/MOTOR/LT_SPARE1',
                          'key': 'actualPosition.value',
                          'dim': None},),
@@ -391,6 +396,79 @@ mnemonics = {
                      'key': 'actualPosition.value',
                      'dim': None},),
 
+    # SHG SETUP in ILH
+    
+    # 800 nm delay line
+    "SHG_DELAY_800": ({'source': 'SCS_GPC_LAS/MOTOR/DELAY',
+                      'key': 'actualPosition.value',
+                      'dim': None},),     
+    # 266 nm attenuator
+    "SHG_ATT_266": ({'source': 'SCS_GPC_MOV/MOTOR/THETA',
+                   'key': 'actualPosition.value',
+                   'dim': None},),
+    # finesse delay stage to find temporal overlap between 800 nm and 400 nm beams
+    "SHG_THG_DELAY": ({'source': 'SCS_LASLAB_LASER/MOTOR/STAGE-4',
+                      'key': 'actualPosition.value',
+                      'dim': None},),     
+    # 266 nm half wave plate otation stage
+    "SHG_HWP_266": ({'source': 'SCS_LASLAB_LASER/MOTOR/STAGE-2',
+                      'key': 'actualPosition.value',
+                      'dim': None},),     
+    # 266 nm lens
+    "SHG_LENS_266": ({'source': 'SCS_GPC_LAS/PMOTOR/PARABOLA_RY',
+                      'key': 'actualPosition.value',
+                      'dim': None},),       
+    # 800 nm attenuator
+    "SHG_ATT_800": ({'source': 'SCS_GPC_MOV/MOTOR/THETAMAG',
+                      'key': 'actualPosition.value',
+                      'dim': None},),
+    # 800 nm HWM
+    "SHG_HWP_800": ({'source': 'SCS_LASLAB_LASER/MOTOR/STAGE-1',
+                      'key': 'actualPosition.value',
+                      'dim': None},),  
+    # 400 nm Glan polarizer
+    "SHG_GLAN_POL": ({'source': 'SCS_LASLAB_LASER/MOTOR/STAGE-3',
+                      'key': 'actualPosition.value',
+                      'dim': None},),      
+    # 800 nm lens
+    "SHG_LENS_800": ({'source': 'SCS_GPC_LAS/PMOTOR/PARABOLA_RZ',
+                      'key': 'actualPosition.value',
+                      'dim': None},),      
+    # sample TX  
+    "SHG_SAM_TX": ({'source': 'SCS_GPC_LAS/PMOTOR/STAGE_X',
+                      'key': 'actualPosition.value',
+                      'dim': None},),  
+    # sample TY
+    "SHG_SAM_TY": ({'source': 'SCS_GPC_LAS/PMOTOR/STAGE_Z',
+                      'key': 'actualPosition.value',
+                      'dim': None},),     
+    # sample RY
+    "SHG_SAM_RY": ({'source': 'SCS_GPC_MOV/MOTOR/X',
+                      'key': 'actualPosition.value',
+                      'dim': None},),    
+    # cameras
+    "SHG_CAM1": ({'source': 'SCS_GPC_SHG/CAM/CAMERA1:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam1_y', 'cam1_x']},),     
+    "SHG_CAM2": ({'source': 'SCS_GPC_SHG/CAM/CAMERA2:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam2_y', 'cam2_x']},), 
+    "SHG_CAM3": ({'source': 'SCS_GPC_SHG/CAM/CAMERA3:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam3_y', 'cam3_x']},), 
+    "SHG_CAM4": ({'source': 'SCS_GPC_SHG/CAM/CAMERA4:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam4_y', 'cam4_x']},),     
+    "SHG_CAM5": ({'source': 'SCS_GPC_SHG/CAM/CAMERA5:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam5_y', 'cam5_x']},), 
+    "SHG_CAM6": ({'source': 'SCS_GPC_SHG/CAM/CAMERA6:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam6_y', 'cam6_x']},), 
+    "SHG_CAM7": ({'source': 'SCS_GPC_SHG/CAM/CAMERA7:daqOutput',
+                      'key': 'data.image.pixels',
+                      'dim': ['cam7_y', 'cam7_x']},),
+
     # GPC
     "GPC_EOS_DelayLine": ({'source': 'SCS_CDIDET_GRD/MOTOR/IMAGER',
                            'key': 'actualPosition.value',