Updated documentation and example scripts

doc-source/conf.py

@@ -58,7 +58,7 @@
 		'rtd': ('https://docs.readthedocs.io/en/latest/', None),
 		'sphinx': ('http://www.sphinx-doc.org/en/stable/', None),
 		'python': ('https://docs.python.org/3/', None),
-		"NumPy": ('https://docs.scipy.org/doc/numpy/', None),
+		"NumPy": ('https://numpy.org/doc/stable/', None),
 		"SciPy": ('https://docs.scipy.org/doc/scipy/reference', None),
 		"matplotlib": ('https://matplotlib.org', None),
 		"h5py": ('https://docs.h5py.org/en/latest/', None),

pyms-demo/jupyter/Peak.ipynb

@@ -192,15 +192,15 @@
    }
   },
   {
-   "cell_type": "raw",
+   "cell_type": "markdown",
    "source": [
     "\n",
     "Mass1-Mass2-Ratio-RT\n"
    ],
    "metadata": {
     "collapsed": false,
     "pycharm": {
-     "name": "#%% raw\n"
+     "name": "#%% md\n"
     }
    }
   },
@@ -386,15 +386,6 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
    "version": "2.7.6"
-  },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "source": [],
-    "metadata": {
-     "collapsed": false
-    }
-   }
   }
  },
  "nbformat": 4,

pyms-demo/scripts/IntensityMatrix.py

@@ -24,7 +24,7 @@
 
 jcamp_file = data_directory / "gc01_0812_066.jdx"
 data = JCAMP_reader(jcamp_file)
-data
+print(data)
 
 
 # Then the data can be converted to an |IntensityMatrix| using the function 
@@ -41,15 +41,15 @@
 
 im = build_intensity_matrix(data)
 
-im
+print(im)
 
 
 # The size as the number of scans and the number of bins can be returned with:
 
 # In[24]:
 
 
-im.size
+print(im.size)
 
 
 # There are 9865 scans and 551 bins in this example.
@@ -61,21 +61,21 @@
 # In[25]:
 
 
-im.mass_list[:10]
+print(im.mass_list[:10])
 
 
 # The attributes |im.min_mass| and |im.max_mass| return the minimum and maximum mass:
 
 # In[26]:
 
 
-im.min_mass
+print(im.min_mass)
 
 
 # In[27]:
 
 
-im.max_mass
+print(im.max_mass)
 
 
 # It is also possible to search for a particular mass, by finding the index of
@@ -88,7 +88,7 @@
 
 index = im.get_index_of_mass(73.3)
 
-index
+print(index)
 
 
 # The value of the closest mass can be returned by the method
@@ -113,21 +113,21 @@
 
 im = build_intensity_matrix(data, 0.5, 0.25, 0.25)
 
-im
+print(im)
 
 
 # The size of the intensity matrix will reflect the change in the number of bins:
 
 # In[31]:
 
 
-im.size
+print(im.size)
 
 
 # In[32]:
 
 
-im.mass_list[:10]
+print(im.mass_list[:10])
 
 
 # In this example there are 9865 scans (as before), but 1101 bins.
@@ -140,7 +140,7 @@
 
 index = im.get_index_of_mass(73.3)
 
-index
+print(index)
 
 
 # In[34]:
@@ -162,19 +162,19 @@
 from pyms.IntensityMatrix import build_intensity_matrix_i
 
 im = build_intensity_matrix_i(data)
-im
+print(im)
 
 
 # In[36]:
 
 
-im.size
+print(im.size)
 
 
 # In[37]:
 
 
-im.mass_list[:10]
+print(im.mass_list[:10])
 
 
 # The masses are now integers.
@@ -183,7 +183,7 @@
 
 
 index = im.get_index_of_mass(73.3)
-index
+print(index)
 
 
 # In[39]:

pyms-demo/scripts/IntensityMatrix_Resizing.py

@@ -71,13 +71,13 @@
 
 
 im.crop_mass(60, 400)
-im.min_mass
+print(im.min_mass)
 
 
 # In[31]:
 
 
-im.max_mass
+print(im.max_mass)
 
 
 # It is also possible to set all intensities for a given mass to zero. This is

pyms-demo/scripts/IonChromatogram.py

@@ -40,7 +40,7 @@
 # In[3]:
 
 
-data.tic
+print(data.tic)
 
 
 # The |IonChromatogram| at index 0 can be obtained with:
@@ -72,4 +72,3 @@
 
 
 im.get_ic_at_mass(73).is_tic()
-

pyms-demo/scripts/MassSpectrum.py

@@ -41,7 +41,7 @@
 
 ms = im.get_ms_at_index(0)
 
-ms
+print(ms)
 
 
 # In[4]:

pyms-demo/scripts/Peak.py

@@ -91,28 +91,30 @@
 # units as given when the Peak object was created). The format is:
 # 
 
-Mass1-Mass2-Ratio-RT
+# 
+# Mass1-Mass2-Ratio-RT
+# 
 
 # For example:
 
 # In[6]:
 
 
-peak.rt
+print(peak.rt)
 
 
 # In[7]:
 
 
-peak.UID
+print(peak.UID)
 
 
 # In[8]:
 
 
 index = im.get_index_of_mass(73.3)
 
-index
+print(index)
 
 
 # ## Modifying a Peak Object
@@ -136,7 +138,7 @@
 # In[10]:
 
 
-peak.UID
+print(peak.UID)
 
 
 # It is also possible to change the peak mass spectrum by setting the attribute |pyms.Peak.Class.Peak.mass_spectrum|.

pyms-demo/scripts/Peak_Area_Estimation.py

@@ -58,7 +58,7 @@
 
 from pyms.BillerBiemann import num_ions_threshold
 filtered_peak_list = num_ions_threshold(peak_list, n=3, cutoff=noise_level)
-filtered_peak_list[:10]
+print(filtered_peak_list[:10])
 
 
 # Given a list of peaks, areas can be determined and added as follows:
@@ -70,4 +70,3 @@
 for peak in peak_list:
     area = peak_sum_area(im, peak)
     peak.area = area
-

pyms-demo/scripts/Peak_Detection.py

@@ -52,7 +52,7 @@
 
 from pyms.BillerBiemann import BillerBiemann
 peak_list = BillerBiemann(im)
-peak_list[:10]
+print(peak_list[:10])
 
 
 # In[20]:
@@ -75,7 +75,7 @@
 
 
 peak_list = BillerBiemann(im, points=9, scans=2)
-peak_list[:10]
+print(peak_list[:10])
 
 
 # In[22]:
@@ -105,14 +105,14 @@
 
 from pyms.BillerBiemann import rel_threshold, num_ions_threshold
 pl = rel_threshold(peak_list, percent=2)
-pl[:10]
+print(pl[:10])
 
 
 # In[24]:
 
 
 new_peak_list = num_ions_threshold(pl, n=3, cutoff=10000)
-new_peak_list[:10]
+print(new_peak_list[:10])
 
 
 # In[25]:

pyms-demo/scripts/Peak_Filtering_Noise_Analysis.py

@@ -59,7 +59,7 @@
 tic = data.tic
 
 noise_level = window_analyzer(tic)
-noise_level
+print(noise_level)
 
 
 # Filter the Peak listusing this noise value as the cutoff.
@@ -70,7 +70,7 @@
 
 from pyms.BillerBiemann import num_ions_threshold
 filtered_peak_list = num_ions_threshold(peak_list, n=3, cutoff=noise_level)
-filtered_peak_list[:10]
+print(filtered_peak_list[:10])
 
 
 # In[4]:

pyms-demo/scripts/comparing_datasets.py

@@ -32,15 +32,15 @@
 
 andi_file = data_directory / "gc01_0812_066.cdf"
 data1 = ANDI_reader(andi_file)
-data1
+print(data1)
 
 
 # In[12]:
 
 
 jcamp_file = data_directory / "gc01_0812_066.jdx"
 data2 = JCAMP_reader(jcamp_file)
-data2
+print(data2)
 
 
 # To compare the two data sets, use the function |diff()|
@@ -68,4 +68,3 @@
 
 
 diff(data1, data2)
-