Merge pull request #42 from spice-herald/feature/offsets_biasflip

Feature/offsets biasflip

Author: magsreed

pytesdaq/io/hdf5.py

@@ -1122,6 +1122,40 @@ def get_detector_config(self, file_name=None,
         return detector_config
 
 
+
+    def get_file_info(self, file_name=None):
+        """
+        Get file attributes
+        """
+
+        # check input 
+        if file_name is None and self._current_file is None:
+            error_msg = 'No file currently open and no "file_name" argument not provided!'
+            if self._raise_errors:
+                    raise ValueError(error_msg)
+            else:
+                print('ERROR: ' + error_msg)
+                print('Please open a file or provide a file name!')
+                return metadata
+
+        # open file if needed
+        if (file_name is not None
+            and self._current_file_name!=file_name):
+            
+            # check if a file already open
+            if self._current_file is not None:
+                self._close_file()
+
+            # open
+            self._open_file(file_name, event_list=None,
+                            load_metadata=False)
+            
+
+        # get attibutes
+        metadata = self._extract_metadata(self._current_file.attrs)
+        return  metadata
+
+    
 
     def get_connection_dict(self, file_name=None, adc_name='adc1', metadata=None):
         """

pytesdaq/processing/__init__.py

@@ -2,3 +2,4 @@
 from ._process_iv_didv import *
 from ._iv_didv_tools_plotting import *
 from ._iv_didv_tools import *
+from .ivsweep import *

pytesdaq/processing/_iv_didv_tools.py

@@ -244,7 +244,8 @@ def _get_current_offset_metadata(metadata, channel_name):
     """
     voltage_offset = metadata[0]['detector_config'][channel_name]['output_offset']
     close_loop_norm = metadata[0]['detector_config'][channel_name]['close_loop_norm']
-    return voltage_offset/close_loop_norm
+    output_gain = metadata[0]['detector_config'][channel_name]['output_gain']
+    return voltage_offset * output_gain/close_loop_norm
 
 class IVanalysis(object):
     """
@@ -1830,7 +1831,8 @@ def plot_noise_model(self, idx='all', xlims=(10, 2e5), ylims_current=None,
         )
 
 
-    def get_offsets_dict(self, metadata, channel_name, lgcdiagnostics=False):
+    def get_offsets_dict(self, metadata, channel_name, lgcdiagnostics=False,
+                        lgc_sweepbias_flipped=False):
         """
         Function to get a dictionary of offsets of i0 and ibias used by
         QETpy to calculate the i0, r0, p0, etc. of a given dIdV.
@@ -1844,6 +1846,16 @@ def get_offsets_dict(self, metadata, channel_name, lgcdiagnostics=False):
 
         channel_name: str
             Used to get the right channel out of the metadata
+            
+        lgcdiagnostics: boolean, optional
+            If True, prints out diagnostics
+            
+        lgc_sweepbias_flipped: boolean, optional
+            Defaults to False. If True, assumes that the bias for the IV sweep
+            from which the offset_dict was generated was flipped in polarity
+            (i.e. multiplied by negative one). To contradict this, we just 
+            multiply the ibias_offset by negative one. Defaults to True because
+            this is the default way we process IV sweeps.
 
         Returns
         -------
@@ -1860,14 +1872,26 @@ def get_offsets_dict(self, metadata, channel_name, lgcdiagnostics=False):
         IV_ibias_offset = self.ivobj.ibias_off[0][1]
         IV_ibias_offset_err = self.ivobj.ibias_off_err[0][1]
 
-        rp_measured = self.df['rp'][0]
+        if lgc_sweepbias_flipped:
+            IV_ibias_offset *= -1
+        
+        i = 0
+        rp_measured = None
+        while rp_measured is None:
+            try:
+                rp_measured = self.df['rp'][i]
+            except KeyError:
+                i += 1
+        
+        output_offset = metadata[0]['detector_config'][channel_name]['output_offset']
 
         return_dict = {
             "i0_off": IV_i0_offset,
             "i0_off_err": IV_i0_offset_err,
             "ibias_off": IV_ibias_offset,
             "ibias_off_err": IV_ibias_offset_err,
             "i0_changable_offset": output_offset_during_didv,
+            "output_offset": output_offset,
             "rp": rp_measured,
             "IVobj": self,
         }