Notebook

Preliminary Runthrough¶

Overview, Import and Example data¶

Take a timespectra and invert all curves after an inflection point in time, then reconstruct data. Removes an inversion induced by particular geometrical parameter in this dataset that otherwise should not be there. I'm going to test a citation here: \cite{Tsai2011} \\

To do: \begin{itemize} \item{Rename flippy\_s function} \item{If time, vectorize "flippy\_s"} \item{Need more robust means to find the inflection point, maybe smooth curves before using?} \end{itemize}

In [3]:

pylab.rcParams['figure.figsize'] = 4,3     #Set plotsize

In [4]:

from skspec import specplot, areaplot, maxmin_xy, absplot
from skspec.IO.gwu_interfaces import from_spec_files, get_files_in_dir
from skspec.exampledata import get_exampledata
import sys

ts = from_spec_files(get_files_in_dir(get_exampledata('NPSAM'),sort=True), name='testname')

Set an arbitrary baseline of 220 counts, a reference and slice to 420.0:700 nm¶

In [5]:

ts.baseline = 220 
ts=ts.ix[420.0:700.0]

ts.sub_base()
ts.reference = 0 #Bug (?) reference must be added after subtraction

specplot(ts)

11-26 14:10:12 CRITICAL skspec.core.timespectra:  Subtracting baseline, but may not have all: elements being equal.  Fix index

Out[5]:

<matplotlib.axes.AxesSubplot at 0x3853550>

Plot Intensity as a function of Time. Each curve corresponds to a certain Wavelength.¶

In [15]:

plt.plot(ts.T)
print type(ts.T)
print ts.T.index

<class 'pandas.core.frame.DataFrame'>
<class 'pandas.tseries.index.DatetimeIndex'>
[2013-09-04 17:28:31, ..., 2013-09-04 17:34:09]
Length: 99, Freq: None, Timezone: None

Plot the area under the curves of raw spectrum against time.¶

In [16]:

areaplot(ts)

11-21 17:56:05 WARNING  skspec.pyplots.basic_plots:  Recomputing area from shape (791, 99) to (1, 99)
11-21 17:56:05 WARNING  skspec.pyplots.basic_plots:  areaplot() forcing transpose on testname for plotting

Out[16]:

<matplotlib.axes.AxesSubplot at 0x9a18d90>

Find out the position of the extremum on the above curve. The flippy analysis here does not use this minimum point. Put it here just incase to use this later. This shows how to find the minimum x value of the area plot¶

In [17]:

tarea = ts.area()
tmin_idx = maxmin_xy(ts.area().T, style='min', arg=False, idx=True, val=False)
tmin_idx

Out[17]:

Wavelength
420.04:699.9   2013-09-04 17:31:20
dtype: datetime64[ns]

Flipping function of a Series: flippy_s, making the plot monotonically decrease or increase.¶

In [18]:

def flippy_s(s,style='decrease'):
    y_flippy_s = [s[0]]
    shift = 0
    for i in range(1,len(s)):
        dy = s[i]-s[i-1]
        
        if style == 'decrease':
            if dy > 0: 
               shift -= 2*dy

        
        elif style == 'increase':
            if dy < 0: 
               shift -= 2*dy
            
        
        else:
            raise AttributeError('style should be decrease and increase')
            
        y_flippy_s.append(s[i]+shift)         
    return y_flippy_s

Apply flippy function of a timespectra¶

In [19]:

ts_1=ts.apply(flippy_s,axis=1)

In [20]:

specplot(ts_1)

Out[20]:

<matplotlib.axes.AxesSubplot at 0x9bebc90>

In [21]:

absplot(ts_1)

Out[21]:

<matplotlib.axes.AxesSubplot at 0x8464390>

In [22]:

absplot(ts)

Out[22]:

<matplotlib.axes.AxesSubplot at 0x8e9cd90>