Renaming of a few fields:

laser_pulse_rate -> laser_repetition_rate alex_period_excitationN -> alex_excitation_periodN See issue Photon-HDF5/photon-hdf5#16.
Photon-HDF5 · Jun 14, 2015 · f9c3a53 · f9c3a53
1 parent 7d671ee
commit f9c3a53
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/notebooks/Convert ns-ALEX Becker-Hickl files to Photon-HDF5.ipynb b/notebooks/Convert ns-ALEX Becker-Hickl files to Photon-HDF5.ipynb
@@ -98,7 +98,7 @@
     "d, meta = phc.loader.nsalex_bh(filename,\n",
     "                               donor = 4,\n",
     "                               acceptor = 6,\n",
-    "                               laser_pulse_rate = 40e6,\n",
+    "                               laser_repetition_rate = 40e6,\n",
     "                               tcspc_range = 60e-9,\n",
     "                               timestamps_unit = 60e-9,\n",
     "                               alex_period_donor = (270, 1500),\n",

diff --git a/phconvert/loader.py b/phconvert/loader.py
@@ -85,7 +85,7 @@ def usalex_sm(
 def nsalex_bh(filename_spc,
               donor = 4,
               acceptor = 6,
-              laser_pulse_rate = 40e6,
+              laser_repetition_rate = 40e6,
               tcspc_range = 60e-9,
               timestamps_unit = 60e-9,
               alex_period_donor = (10, 1500),
@@ -159,7 +159,7 @@ def nsalex_bh(filename_spc,
 
         measurement_specs = dict(
             measurement_type = 'smFRET-nsALEX',
-            laser_pulse_rate = laser_pulse_rate,
+            laser_repetition_rate = laser_repetition_rate,
             alex_period_excitation1 = alex_period_donor,
             alex_period_excitation2 = alex_period_acceptor,
             detectors_specs = dict(spectral_ch1 = donor,
@@ -208,7 +208,7 @@ def nsalex_ht3(filename,
     tcspc_unit = metadata.pop('nanotimes_unit')
     tcspc_num_bins = 4096
     tcspc_range = tcspc_num_bins*tcspc_unit
-    laser_pulse_rate = metadata['ttmode']['SyncRate']
+    laser_repetition_rate = metadata['ttmode']['SyncRate']
     acquisition_time = metadata['header']['Tacq'][0]*1e-3
     software = metadata['header']['CreatorName']
     software_version = metadata['header']['CreatorVersion']
@@ -240,7 +240,7 @@ def nsalex_ht3(filename,
 
         measurement_specs = dict(
             measurement_type = 'smFRET-nsALEX',
-            laser_pulse_rate = laser_pulse_rate,
+            laser_repetition_rate = laser_repetition_rate,
             alex_period_excitation1 = alex_period_donor,
             alex_period_excitation2 = alex_period_acceptor,
             detectors_specs = dict(spectral_ch1 = donor,

diff --git a/phconvert/specs/photon-hdf5_fields.json b/phconvert/specs/photon-hdf5_fields.json
@@ -35,13 +35,13 @@
         "Name of the measurement the data represents.",
     "/photon_data/measurement_specs/alex_period":
         "Period of laser alternation in us-ALEX measurements in timestamps units.",
-    "/photon_data/measurement_specs/laser_pulse_rate":
+    "/photon_data/measurement_specs/laser_repetition_rate":
         "Repetition rate of the pulsed excitation laser.",
     "/photon_data/measurement_specs/alex_offset":
         "Time offset (in timestamps unit) to apply to timestamps to obtain a properly aligned alternation histogram.",
-    "/photon_data/measurement_specs/alex_period_excitation1":
+    "/photon_data/measurement_specs/alex_excitation_period1":
         "Values pair (start-stop range) identifying photons in the excitation period of wavelength 1 (the shortest).",
-    "/photon_data/measurement_specs/alex_period_excitation2":
+    "/photon_data/measurement_specs/alex_excitation_period2":
         "Values pair (start-stop range) identifying photons in the excitation period of wavelength 2.",
     "/photon_data/measurement_specs/detectors_specs":
         "Mapping between the detector IDs and the detection channels.",