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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 100412 (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__ = "100412"
21 > __version__ = "110204"
22 >
23  
24   ## Import libraries.
25   import numpy as np
26 < import matplotlib.pyplot as plt
26 > #import matplotlib.pyplot as plt
27   from datetime import date
28  
29  
30   class BiosensorArray(object):
31 <    """The Biosensor Array class holds all ROIs/spots from an SPRI microarray run."""
31 >    """
32 >    The Biosensor Array class holds all ROIs (spots)
33 >    from an SPRI microarray run.
34 >    
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):
47          """This object is dimensioned upon initialization.""" ## Might improve speed.
48          ## Use a list comprehension to dimension list of classes.
# Line 30 | 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 42 | 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 63 | 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 <    """This Region Of Interest class can hold one SPR sensorgram."""
98 >    """
99 >    This Region Of Interest class can hold one SPR sensorgram.
100 >    
101 >    =========== =============== =============================================
102 >    Property    Type            Description
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.
107 >    value       nparray         Arbitrary units.
108 >    dpoints     integer         Can use for bounds checking.
109 >    name        string          Name of ROI.
110 >    desc        string          Description of ROI
111 >    
112 >    gridx       integer         Can be Block number from GAL file.  
113 >    gridy       integer         Unused?
114 >    spotx       integer         ROI column number.
115 >    spoty       integer         ROI row number.
116 >    bgroi       list of integer One or more background ROIs.
117 >    calibM      float           Slope used for calibration
118 >    calibB      float           Intercept used for calibration.
119 >    plottable   boolean         Whether to plot
120 >    
121 >    injconc     list of float   One or more analyte concentrations.
122 >    injstart    list of float   One or more injection start times.
123 >    injstop     list of float   One or more injection start times.
124 >    injrind     list of float   One or more expected refractive index jumps.
125 >    
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):
133          """
134          Each ROI in a list needs a unique ID number which will be i+1.
# Line 95 | Line 156
156          self.injstop = [0.0]     ## One or more injection start times.
157          self.injrind = [0.0]     ## One or more expected refractive index jumps.
158          self.flow = 0            ## Flowrate of injection.
159 +        ## Curve fitting information.  Model and model parameters.
160 +        ## Example model is reference to function like data=simple1to1(times,params)
161 +        ## Example params = {'Rmax': {'value':1, 'min':0, 'max':10, 'fixed':'float'} }
162 +        self.model = None    ## Model describing this roi. Reference to a function.
163 +        self.params = []     ## Parameters for this model. A dictionary of dictionaries.
164          
165      def time2dp(self, t):
166          """Find datapoint closest to given time."""
167 <        pos2 = self.time.searchsorted(t)  ## Time point just after t.
168 <        pos1 = max(pos2-1,0)
169 <        #TEMP! There is a bug here.
104 <        print pos1, pos2
167 >        pos2 = self.time.searchsorted(t)    ## Time point just after t.
168 >        pos2 = min(pos2, len(self.time)-1)  ## Avoid indexing error.
169 >        pos1 = max(pos2-1,0)                ## Time point just before t.
170          t2 = abs(self.time[pos2] - t)
171          t1 = abs(self.time[pos1] - t)
172 +        ## Decide if time point just before or just after is closer.
173          if (t2<t1):
174              return pos2
175          else:
# Line 112 | Line 178
178      def time2val(self, t1, t2):
179          """Return list of SPR values between t1 and t2"""
180          dp1, dp2 = self.time2dp(t1), self.time2dp(t2)
181 <        return [self.value(i) for i in range(dp1, dp2)]
181 >        return [self.value[i] for i in range(dp1, dp2)]
182      
183 <    ## End of RegOfInterest definition.
118 <
183 >    """End of RegOfInterest definition."""
184  
185 + '''
186   ## Here are a few lines to test this class.
187   if __name__ == '__main__':
188      print "Starting demo..."
# Line 137 | Line 203
203      print "Test time2dp... 5.6 =>",
204      print x.roi[9].time2dp(5.6)
205      print "Demo finished."
206 + '''
207      
208      
142 ################################# End of module #################################
209 + ################################# End of module #################################

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