This is the official Ionicon Python toolbox for proton-transfer reaction mass-spectrometry (PTR-MS).
Install from PyPI (see also getting started):
>> pip install -U pytrmsFor simple analysis tasks use the PyTRMS Python package to read and analyse Ionicon
hdf5 files. The Pandas
Python package is the de-facto standard for data analysis. Use PyTRMS to load the
traces directly into a Pandas.DataFrame.
In the following example, the traces (i.e. timeseries data) is loaded from a datafile. We are looking for traces containing the term 'H2O' and print out some statistics:
>>> import pytrms
>>> import pandas as pd
>>> measurement = pytrms.load('examples/data/peter_emmes_2022-03-31_08-51-13.h5')
>>> traces = measurement.read_traces('concentration')
>>> water_columns = [col for col in traces.columns if 'H2O' in col]
>>> for col_name in sorted(water_columns): print(col_name)
*(FeH2O2)H+
*(H2O)+
*(H2O)2H+
*(H2O)2H+ i_17O
*(H2O)2H+ i_18O
*(H2O)3H+
*(H2O)3H+ i_18O
*(H2O)4H+
*(H2O)H+
*(H2O)H+ i_18O
H2O.H3O+ (Cluster)
H2O_Act
H2O_Set
>>> traces[['H2O.H3O+ (Cluster)', 'm046_o', 'm089_o', 'H2O_Act']].describe()
H2O.H3O+ (Cluster) m046_o m089_o H2O_Act
count 129.000000 129.000000 129.000000 129.000000
mean 11.239826 10.229387 2.553549 5.001189
std 9.276476 1.901914 1.029452 0.000408
min 1.928841 7.397606 1.066777 5.000156
25% 2.486116 8.636315 1.566666 5.001094
50% 8.096381 9.788801 2.517548 5.001094
75% 18.895479 11.597718 3.342328 5.001563
max 28.722771 14.569857 4.773218 5.002031After processing the sourcefile with the Ionicon PTRMS Viewer we get a slightly different result for mass 46.0, because the peak was optimized...
>>> measurement = pytrms.load('examples/data/processed/peter_emmes_2022-03-31_08-51-13.h5')
>>> traces = measurement.read_traces()
>>> traces[['H2O.H3O+ (Cluster)', 'm046_o']].mean()
H2O.H3O+ (Cluster) 11.239826
m046_o 10.239784
dtype: float32...but the original measurement can still be read if we insist to:
>>> traces = measurement.read_traces(force_original=True)
>>> traces[['H2O.H3O+ (Cluster)', 'm046_o']].mean()
H2O.H3O+ (Cluster) 11.239826
m046_o 10.229387
dtype: float32When analysing a bunch of datafiles, we can use a glob-expression to collect files from a directory tree and let PyTRMS sort our batch by the start time:
>>> batch = pytrms.load('examples/data/peter_emmes*.h5')
>>> for sourcefile in batch: print(sourcefile) # doctest: +ELLIPSIS
<...examples/data\peter_emmes_2022-03-31_08-51-13.h5>
<...examples/data\peter_emmes_2022-03-31_08-59-30.h5>
<...examples/data\peter_emmes_2022-03-31_09-10-08.h5>
<...examples/data\peter_emmes_2022-03-31_09-20-31.h5>
<...examples/data\peter_emmes_2022-03-31_09-29-40.h5>
>>> len(batch)
5When performing many consecutive and repetitive measurements, it is desirable to get
repeatable results. With the PyTRMS package, measurements can be easily scripted.
For example, perform ten measurements of one minute each and save the datafiles in a folder. The filename is automatically set to the timestamp at the start of the measurement.
>>> import pytrms
# initialize a connection to a PTR instrument server
# (this would assume that IoniTOF is running locally,
# but you could also pass in a network address):
>>> ptr = pytrms.connect('localhost') # doctest: +ELLIPSIS +SKIP
<pytrms.instrument.IdleInstrument object at 0x...>
>>> ptr # doctest: +ELLIPSIS +SKIP
<pytrms.instrument.IdleInstrument object at 0x...>
# the instrument is idle, let's start a measurement!
# when passing a filename it may contain placeholders
# such as %Y, %m, %d that will be filled with the current
# date and time (google strftime for details):
>>> ptr.start_measurement('pytrms-test/%Y/%m/') # doctest: +ELLIPSIS +SKIP
<pytrms.instrument.RunningInstrument object at 0x...>
>>> ptr.wait(10, 'collecting data for ten seconds...') # doctest: +SKIP
collecting data for a ten seconds...
# we got enough data, let's stop the measurement:
>>> ptr.stop_measurement() # doctest: +ELLIPSIS +SKIP
<pytrms.instrument.IdleInstrument object at 0x...>Download and install the latest Python version if you have not done so. Ionicon recommends to download Python 3.12 for Windows. This will install the Python executable along with the package manager pip. Using pip is the preferred way to get the latest version of PyTRMS, but other solutions like Anaconda should also work. In a terminal type
python -m pip install -U pytrms
to install the latest release from PyPI. This command can also be used at any later time to upgrade to the newest version.
Download and extract the examples folder (by clicking on Code and selecting
Download ZIP from the dropdown menu).
The Python scripts can be run by simply double-clicking them.
If something is not working correctly, the setup may be broken.
Repeat the steps from the Getting started
section and make sure to use the default options.
For testing purposes it is strongly recommended to install the PyTRMS package in a fresh
virtual environment, separated from the system-wide installed Python packages.
If you have installed Python Poetry,
managing the dependencies is a breeze. In the pytrms folder type poetry install to
install the PyTRMS package and its dependencies in a fresh virtual environment. To then
use any python command in this virtual environment, simply prefix it with poetry run,
for example like this:
> poetry run python examples\breath_tracking.py
Without poetry, create and activate a fresh virtual environment, then install the requirements:
> python -m venv test-pytrms
> .\test-pytrms\bin\activate
> python -m pip install -r examples\REQUIRES.txtYou may now run the examples like this:
> python examples\breath_tracking.pyNote, that the online examples assume that you have a Ionicon PTR-MS connected to your PC and running the which is running a ioniTOF server with the Ionicon webAPI.