pytrms 0.9.2__py3-none-any.whl → 0.9.3__py3-none-any.whl

pytrms/measurement.py

@@ -1,173 +1,173 @@
-import time
-from operator import attrgetter
-from itertools import chain
-from abc import abstractmethod, ABC
-
-import pandas as pd
-
-from .readers import IoniTOFReader
-
-__all__ = ['Measurement', 'PreparingMeasurement', 'RunningMeasurement', 'FinishedMeasurement']
-
-
-class Measurement(ABC):
-    """Class for PTRMS-measurements and batch processing.
-
-    The start time of the measurement is given by `.time_of_meas`.
-
-    A measurement is iterable over the 'rows' of its data. 
-    In the online case, this would slowly produce the current trace, one
-    after another.
-    In the offline case, this would quickly iterate over the traces in the given
-    measurement file.
-    """
-
-    def _new_state(self, newstate):
-        # Note: we get ourselves a nifty little state-machine :)
-        self.__class__ = newstate
-
-    def start(self, filename=''):
-        """Start a measurement on the PTR server.
-
-        'filename' is the filename of the datafile to write to. 
-        If left blank, start a "quick measurement".
-
-        If pointing to a file and the file exist on the (local) server, this raises an exception.
-        To create unique filenames, use placeholders for year (%Y), month (%m), and so on,
-        for example `filename=C:/Ionicon/Data/Sauerteig_%Y-%m-%d_%H-%M-%S.h5`.
-
-        see also:
-        """
-        # this method must be implemented by each state
-        raise RuntimeError("can't start %s" % self.__class__)
-
-    # (see also: this docstring)
-    start.__doc__ += time.strftime.__doc__
-
-    def stop(self):
-        """Stop the current measurement on the PTR server."""
-        raise RuntimeError("can't stop %s" % self.__class__)
-
-    @abstractmethod
-    def __len__(self):
-        pass
-
-
-class PreparingMeasurement(Measurement):
-
-    @property
-    def single_spec_duration_ms(self):
-        return self.ptr.get('ACQ_SRV_SpecTime_ms')
-
-    @single_spec_duration_ms.setter
-    def single_spec_duration_ms(self, value):
-        self.ptr.set('ACQ_SRV_SpecTime_ms', int(value), unit='ms')
-
-    @property
-    def extraction_time_us(self):
-        return self.ptr.get('ACQ_SRV_ExtractTime')
-
-    @extraction_time_us.setter
-    def extraction_time_us(self, value):
-        self.ptr.set('ACQ_SRV_ExtractTime', int(value), unit='us')
-
-    @property
-    def max_flight_time_us(self):
-        return self.ptr.get('ACQ_SRV_MaxFlighttime')
-
-    @max_flight_time_us.setter
-    def max_flight_time_us(self, value):
-        self.ptr.set('ACQ_SRV_MaxFlighttime', int(value), unit='us')
-
-    @property
-    def expected_mass_range_amu(self):
-        return self.ptr.get('ACQ_SRV_ExpectMRange')
-
-    @expected_mass_range_amu.setter
-    def expected_mass_range_amu(self, value):
-        self.ptr.set('ACQ_SRV_ExpectMRange', int(value), unit='amu')
-
-    def __init__(self, instrument):
-        self.ptr = instrument
-
-    def start(self, filename=''):
-        self.ptr.start_measurement(filename)
-        self._new_state(RunningMeasurement)
-
-    def __len__(self):
-        return 0
-
-
-class RunningMeasurement(Measurement):
-
-    def __init__(self, instrument):
-        self.ptr = instrument
-
-    def stop(self):
-        self.ptr.stop_measurement()
-        self._new_state(FinishedMeasurement)
-
-    def __len__(self):
-        return -1
-
-
-class FinishedMeasurement(Measurement):
-
-    @classmethod
-    def _check(cls, sourcefiles):
-        _assumptions = ("incompatible files! "
-                "sourcefiles must have the same number-of-timebins and "
-                "the same instrument-type to be collected as a batch")
-
-        assert 1 == len(set(sf.inst_type          for sf in sourcefiles)), _assumptions
-        assert 1 == len(set(sf.number_of_timebins for sf in sourcefiles)), _assumptions
-
-    @property
-    def number_of_timebins(self):
-        return next(iter(self.sourcefiles)).number_of_timebins
-
-    @property
-    def poisson_deadtime_ns(self):
-        return next(iter(self.sourcefiles)).poisson_deadtime_ns
-
-    @property
-    def pulsing_period_ns(self):
-        return next(iter(self.sourcefiles)).pulsing_period_ns
-
-    @property
-    def single_spec_duration_ms(self):
-        return next(iter(self.sourcefiles)).single_spec_duration_ms
-
-    @property
-    def start_delay_ns(self):
-        return next(iter(self.sourcefiles)).start_delay_ns
-
-    @property
-    def timebin_width_ps(self):
-        return next(iter(self.sourcefiles)).timebin_width_ps
-
-    def __init__(self, *filenames, _reader=IoniTOFReader):
-        if not len(filenames):
-            raise ValueError("no filename given")
-
-        self.sourcefiles = sorted((_reader(f) for f in filenames), key=attrgetter('time_of_file'))
-        self._check(self.sourcefiles)
-
-    def read_traces(self, kind='conc', index='abs_cycle', force_original=False):
-        """Return the timeseries ("traces") of all masses, compounds and settings.
-
-        'kind' is the type of traces and must be one of 'raw', 'concentration' or
-        'corrected'.
-
-        'index' specifies the desired index and must be one of 'abs_cycle', 'rel_cycle',
-        'abs_time' or 'rel_time'.
-
-        """
-        return pd.concat(sf.read_all(kind, index, force_original) for sf in self.sourcefiles)
-
-    def __iter__(self):
-        return iter(self.sourcefiles)
-
-    def __len__(self):
-        return len(self.sourcefiles)
-
+import time
+from operator import attrgetter
+from itertools import chain
+from abc import abstractmethod, ABC
+
+import pandas as pd
+
+from .readers import IoniTOFReader
+
+__all__ = ['Measurement', 'PreparingMeasurement', 'RunningMeasurement', 'FinishedMeasurement']
+
+
+class Measurement(ABC):
+    """Class for PTRMS-measurements and batch processing.
+
+    The start time of the measurement is given by `.time_of_meas`.
+
+    A measurement is iterable over the 'rows' of its data. 
+    In the online case, this would slowly produce the current trace, one
+    after another.
+    In the offline case, this would quickly iterate over the traces in the given
+    measurement file.
+    """
+
+    def _new_state(self, newstate):
+        # Note: we get ourselves a nifty little state-machine :)
+        self.__class__ = newstate
+
+    def start(self, filename=''):
+        """Start a measurement on the PTR server.
+
+        'filename' is the filename of the datafile to write to. 
+        If left blank, start a "quick measurement".
+
+        If pointing to a file and the file exist on the (local) server, this raises an exception.
+        To create unique filenames, use placeholders for year (%Y), month (%m), and so on,
+        for example `filename=C:/Ionicon/Data/Sauerteig_%Y-%m-%d_%H-%M-%S.h5`.
+
+        see also:
+        """
+        # this method must be implemented by each state
+        raise RuntimeError("can't start %s" % self.__class__)
+
+    # (see also: this docstring)
+    start.__doc__ += time.strftime.__doc__
+
+    def stop(self):
+        """Stop the current measurement on the PTR server."""
+        raise RuntimeError("can't stop %s" % self.__class__)
+
+    @abstractmethod
+    def __len__(self):
+        pass
+
+
+class PreparingMeasurement(Measurement):
+
+    @property
+    def single_spec_duration_ms(self):
+        return self.ptr.get('ACQ_SRV_SpecTime_ms')
+
+    @single_spec_duration_ms.setter
+    def single_spec_duration_ms(self, value):
+        self.ptr.set('ACQ_SRV_SpecTime_ms', int(value), unit='ms')
+
+    @property
+    def extraction_time_us(self):
+        return self.ptr.get('ACQ_SRV_ExtractTime')
+
+    @extraction_time_us.setter
+    def extraction_time_us(self, value):
+        self.ptr.set('ACQ_SRV_ExtractTime', int(value), unit='us')
+
+    @property
+    def max_flight_time_us(self):
+        return self.ptr.get('ACQ_SRV_MaxFlighttime')
+
+    @max_flight_time_us.setter
+    def max_flight_time_us(self, value):
+        self.ptr.set('ACQ_SRV_MaxFlighttime', int(value), unit='us')
+
+    @property
+    def expected_mass_range_amu(self):
+        return self.ptr.get('ACQ_SRV_ExpectMRange')
+
+    @expected_mass_range_amu.setter
+    def expected_mass_range_amu(self, value):
+        self.ptr.set('ACQ_SRV_ExpectMRange', int(value), unit='amu')
+
+    def __init__(self, instrument):
+        self.ptr = instrument
+
+    def start(self, filename=''):
+        self.ptr.start_measurement(filename)
+        self._new_state(RunningMeasurement)
+
+    def __len__(self):
+        return 0
+
+
+class RunningMeasurement(Measurement):
+
+    def __init__(self, instrument):
+        self.ptr = instrument
+
+    def stop(self):
+        self.ptr.stop_measurement()
+        self._new_state(FinishedMeasurement)
+
+    def __len__(self):
+        return -1
+
+
+class FinishedMeasurement(Measurement):
+
+    @classmethod
+    def _check(cls, sourcefiles):
+        _assumptions = ("incompatible files! "
+                "sourcefiles must have the same number-of-timebins and "
+                "the same instrument-type to be collected as a batch")
+
+        assert 1 == len(set(sf.inst_type          for sf in sourcefiles)), _assumptions
+        assert 1 == len(set(sf.number_of_timebins for sf in sourcefiles)), _assumptions
+
+    @property
+    def number_of_timebins(self):
+        return next(iter(self.sourcefiles)).number_of_timebins
+
+    @property
+    def poisson_deadtime_ns(self):
+        return next(iter(self.sourcefiles)).poisson_deadtime_ns
+
+    @property
+    def pulsing_period_ns(self):
+        return next(iter(self.sourcefiles)).pulsing_period_ns
+
+    @property
+    def single_spec_duration_ms(self):
+        return next(iter(self.sourcefiles)).single_spec_duration_ms
+
+    @property
+    def start_delay_ns(self):
+        return next(iter(self.sourcefiles)).start_delay_ns
+
+    @property
+    def timebin_width_ps(self):
+        return next(iter(self.sourcefiles)).timebin_width_ps
+
+    def __init__(self, *filenames, _reader=IoniTOFReader):
+        if not len(filenames):
+            raise ValueError("no filename given")
+
+        self.sourcefiles = sorted((_reader(f) for f in filenames), key=attrgetter('time_of_file'))
+        self._check(self.sourcefiles)
+
+    def read_traces(self, kind='conc', index='abs_cycle', force_original=False):
+        """Return the timeseries ("traces") of all masses, compounds and settings.
+
+        'kind' is the type of traces and must be one of 'raw', 'concentration' or
+        'corrected'.
+
+        'index' specifies the desired index and must be one of 'abs_cycle', 'rel_cycle',
+        'abs_time' or 'rel_time'.
+
+        """
+        return pd.concat(sf.read_all(kind, index, force_original) for sf in self.sourcefiles)
+
+    def __iter__(self):
+        return iter(self.sourcefiles)
+
+    def __len__(self):
+        return len(self.sourcefiles)
+