from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.TopHat import tophat
# In[2]:
cwd = PathPlus('.').resolve()
data_directory = PathPlus('.').resolve().parent.parent / "datafiles"
# Change this if the data files are stored in a different location
output_directory = cwd / "output"
# In[3]:
jcamp_file = data_directory / "gc01_0812_066.jdx"
data = JCAMP_reader(jcamp_file)
data.trim("500s", "2000s")
tic = data.tic
im = build_intensity_matrix(data)
# In[4]:
n_scan, n_mz = im.size
for ii in range(n_mz):
ic = im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
im.set_ic_at_index(ii, ic_bc)
# In[5]:
andi_file = data_directory / "gc01_0812_066.cdf" data1 = ANDI_reader(andi_file) print(data1) # In[3]: jcamp_file = data_directory / "gc01_0812_066.jdx" data2 = JCAMP_reader(jcamp_file) print(data2) # To compare the two data sets, use the function |diff()| # In[4]: from pyms.GCMS.Function import diff diff(data1, data2) # If the data cannot be compared, for example because of # different number of scans, or inconsistent number of m/z values # in between two scans, |diff()| # will report the difference. For example: # In[5]: data2.trim(begin=1000, end=2000) # In[6]: diff(data1, data2)
jcamp_file = data_directory / "gc01_0812_066.jdx"
data = JCAMP_reader(jcamp_file)
im = build_intensity_matrix(data)
# ## Retention time range
#
# A basic operation on the GC-MS data is to select a specific time range for
# processing. In PyMassSpec, any data outside the chosen time range is discarded.
# The |trim()| method operates on the raw data, so any subsequent processing only
# refers to the trimmed data.
#
# The data can be trimmed to specific scans:
# In[3]:
data.trim(1000, 2000)
data.info()
# or specific retention times (in ``seconds`` or ``minutes``):
# In[4]:
data.trim("700s", "15m")
data.info()
# ## Mass Spectrum range and entries
#
# An |IntensityMatrix| object has a set mass range and interval that is derived
# from the data at the time of building the intensity matrix. The range of mass
# values can be cropped. This is done, primarily, to ensure that the range of
# masses used are consistent when comparing samples.
