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# Line 1 | Line 1
1   """
2 < ba: Biosensor Array class for storing SPRI data.
3 < Christopher Lausted, Institute for Systems Biology,
4 < Yuhang Wan, OSPRAI developers
5 < Last modified on 100517 (yymmdd)
6 <
7 < Examples:
8 < #ba1 = BiosensorArray(800,1500)     ## Allocate object with 800 spots of 1500 time points.
9 < #ba1.roi[799].time[1499] = 7502.1   ## Set time in seconds.
10 < #ba1.roi[799].value[1499] = 0.50    ## Set SPR reflectance signal.
11 < #ba1.roi[799].name = "anti-IgG"     ## Set name of microarray feature.
2 > ba_class
3 > --------
4 >
5 > Biosensor Array class for storing SPRI data.
6 > This contains an array of SPR sensorgrams with their
7 > associated models and parameters.
8 > This can also contain the microarray geometery.
9 >
10 > .. moduleauthor:: Christopher Lausted,
11 >                  Institute for Systems Biology,
12 >                  Yuhang Wan,
13 >                  OSPRAI developers.  
14 >                  
15 > Examples::
16 >  >>> ba1 = BiosensorArray(800,1500)     ## Allocate object with 800 spots of 1500 time points.
17 >  >>> ba1.roi[799].time[1499] = 7502.1   ## Set time in seconds.
18 >  >>> ba1.roi[799].value[1499] = 0.50    ## Set SPR reflectance signal.
19 >  >>> ba1.roi[799].name = "anti-IgG"     ## Set name of microarray feature.
20   """
21 < __version__ = "100517"
21 > __version__ = "110204"
22 >
23  
24   ## Import libraries.
25   import numpy as np
# Line 23 | Line 32
32      The Biosensor Array class holds all ROIs (spots)
33      from an SPRI microarray run.
34      
35 <    Property    Type            Description
36 <    --------    --------------  ---------------------------------------
37 <    roi         list of object  List of RegOfInterest objects.
38 <    rois        integer         Size of roi (Number of ROIs).
39 <    dpoints     integer         Number of datapoints in each ROI.
40 <    primarydatafiles            List of file names.
41 <    comments    list of string  List of comments regarding experiments.
35 >    ================ =============== =======================================
36 >    Property         Type            Description
37 >    ---------------- --------------- ---------------------------------------
38 >    roi              list of object  List of RegOfInterest objects.
39 >    rois             integer         Size of roi (Number of ROIs).
40 >    dpoints          integer         Number of datapoints in each ROI.
41 >    primarydatafiles list of string  List of file names.
42 >    comments         list of string  List of comments regarding experiments.
43 >    ================ =============== =======================================
44      """
45      
46      def __init__(self, roi_size, datapoint_size):
# Line 42 | Line 53
53          ## Use these to keep track of laboratory notes.
54          self.primarydatafiles = [""]  ## Like "spritdata.txt"
55          self.comments = [""]          ## Like "Antibody data from 1 Jan 2010"
56 +        return
57          
58      def xy2uid(self, gx, gy, x, y):
59          """Given roi coordinates, find corresponding uid (index)."""
# Line 54 | Line 66
66      def set_plot_all(self):
67          """Choose to plot every sensorgram."""
68          for ob in self.roi: ob.plottable = True
69 +        return
70          
71      def set_plot_list(self, ilist):
72          """Choose a list of sensorgrams to plot"""
73          for ob in self.roi: ob.plottable = False
74          for i in ilist: self.roi[i].plottable = True
75 <    
75 >        return
76 >        
77      ## A pyplot feature for testing purposes.
78      def plot(self):
79          """Show plot of the selected sensorgrams."""
# Line 75 | Line 89
89                  plt.plot(ob.time, ob.value, label=mylabel)
90          plt.legend(loc='best')
91          plt.show()
92 <    ### End of BiosensorArray class definition.
92 >        return
93 >        
94 >    """End of BiosensorArray class definition."""
95  
96  
97   class RegOfInterest(object):
98      """
99      This Region Of Interest class can hold one SPR sensorgram.
100      
101 +    =========== =============== =============================================
102      Property    Type            Description
103 <    --------    --------------  ---------------------------------------------
103 >    ----------- --------------- ---------------------------------------------
104      uid         integer         Unique ID integer. Never changes.
105      index       integer         Changes if ba size changes (add/remove rois).
106      time        nparray         Usually seconds.
# Line 109 | Line 126
126      flow        float           Flowrate of injection.
127      model       ref to funct    Model describing this ROI.
128      params      dict of dict    Parameters for this model.
129 +    =========== =============== =============================================
130      """
131      
132      def __init__(self, i, datapoint_size):
# Line 162 | Line 180
180          dp1, dp2 = self.time2dp(t1), self.time2dp(t2)
181          return [self.value[i] for i in range(dp1, dp2)]
182      
183 <    ## End of RegOfInterest definition.
183 >    """End of RegOfInterest definition."""
184  
185   '''
186   ## Here are a few lines to test this class.

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