Add config file comments

specsanalyzer/config/default.yaml

@@ -1,9 +1,18 @@
+# path to SPECS calib2d file (provided together with your analyzer)
 calib2d_file: "./config/phoibos150.calib2d"
+# number of pixels along the energy dispersing direction
 nx_pixel: 1376
+# number of pixels along the angle/spatially dispersing direction
 ny_pixel: 1024
+# pixel size in millimeters
 pixel_size: 0.00645
+# binning factor applied to the image
 binning: 4
+# magnification of the lens system used for imaging the detector
 magnification: 4.54
-Ang_Offset_px: 0
-E_Offset_px: 0
-apply_fft_filter: False
+# offset in pixels along the angular dispersing axis
+angle_offset_px: 0
+# offset in pixels along the energy dispersing axis
+energy_offset_px: 0
+# flag controlling the application of a Fourier filter to remove grid artefacts
+apply_fft_filter: false

specsscan/config/default.yaml

@@ -1,8 +1,12 @@
-data_path: "//nap32/topfloor/trARPES/PESData/"
+# path to the default data directory
+data_path: ""
+# option to enable nested progress bars
 enable_nested_progress_bar: false
+# dictionary containing parameters passed to the SpecsAnalyzer. Will be completed by the SpecsAnalyzer default config parameters
 spa_params:
   apply_fft_filter: false
 
+# dictionary containing units for the respective axes
 units:
   Angle: "degree"
   Ekin: "eV"

specsscan/config/example_config_FHI.yaml

@@ -1,6 +1,9 @@
+# path to the default data directory
 data_path: "path/to/data"
+# option to enable nested progress bars
 enable_nested_progress_bar: false
 
+# dictionary containing renaming rules for axis names (to change the name in the xarrays)
 coordinate_mapping:
   Ekin: "energy"
   Angle: "angular1"
@@ -11,6 +14,7 @@ coordinate_mapping:
   Y: "spatial1"
   Z: "spatial1"
 
+# dictionary of corresponding NeXus paths for the different axes
 coordinate_depends:
   Ekin: "/entry/instrument/electronanalyser/energydispersion/kinetic_energy"
   Angle: "/entry/instrument/electronanalyser/transformations/analyzer_dispersion"
@@ -21,6 +25,7 @@ coordinate_depends:
   Y: "/entry/sample/transformations/trans_y"
   Z: "/entry/sample/transformations/trans_z"
 
+# dictionary containing units for the respective axes
 units:
   angular1: "degree"
   angular2: "degree"
@@ -33,6 +38,9 @@ units:
   Z: "mm"
   voltage: "V"
 
+# URL of the epics archiver request engine
+archiver_url: "http://__epicsarchiver_host__:17668/retrieval/data/getData.json?pv="
+# dictionary containing axis names with Epics channels to request from the EPICS archiver
 epics_channels:
   tempa: "trARPES:Carving:TEMP_RBV"
   x: "trARPES:Carving:TRX.RBV"
@@ -44,19 +52,38 @@ epics_channels:
   drain_current: "trARPES:Sample:Measure"
   pressure: "trARPES:XGS600:PressureAC:P_RD"
 
+# parameters for NeXus conversion
 nexus:
+  # the reader to use
   reader: "mpes"
+  # the NeXus definition to use
   definition: "NXmpes"
+  # additional input files, e.g. config and ELN files
   input_files: ["../specsscan/config/NXmpes_arpes_config.json"]
 
+# parameters for the SpecsAnalyzer
 spa_params:
+  # path to SPECS calib2d file (provided together with your analyzer)
   calib2d_file: "../tests/data/phoibos150.calib2d"
+  # number of pixels along the energy dispersing direction
   nx_pixel: 1376
+  # number of pixels along the angle/spatially dispersing direction
   ny_pixel: 1024
+  # pixel size in millimeters
   pixel_size: 0.00645
+  # binning factor applied to the image
+  binning: 4
+  # magnification of the lens system used for imaging the detector
   magnification: 4.54
+  # option for cropping the resulting xarrays
   crop: false
+  # option to apply Fourier filtering
   apply_fft_filter: true
+  # dictionary containing definition for Gaussian Fourier peaks to subtract.
+  # each entry defines:
+  #   amplitude: the normalized peak amplitude
+  #   pos_x/pos_y: the peak position in Fourier plane pixels
+  #   sigma_x/sigma_y: the peak width (standard deviation) along each direction
   fft_filter_peaks:
     - amplitude: 1
       pos_x: 79