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root/osprai/osprai/trunk/ba_class.py
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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 100409 (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 >
17 >  >>> ba1 = BiosensorArray(800,1500)     ## Allocate object with 800 spots of 1500 time points.
18 >  >>> ba1.roi[799].time[1499] = 7502.1   ## Set time in seconds.
19 >  >>> ba1.roi[799].value[1499] = 0.50    ## Set SPR reflectance signal.
20 >  >>> ba1.roi[799].name = "anti-IgG"     ## Set name of microarray feature.
21   """
22 < __version__ = "100409"
22 > __version__ = "110208"
23 >
24  
25   ## Import libraries.
26   import numpy as np
17 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)."""
60          coor1 = (gx, gy, x, y)
61 <        for ob in self.roi:
62 <            coor2 = (ob.gridx, ob.gridy, ob.spotx, ob.spoty)
63 <            if (coor1==coor2): return ob.uid  ## Success.
61 >        for roi in self.roi:
62 >            coor2 = (roi.gridx, roi.gridy, roi.spotx, roi.spoty)
63 >            if (coor1==coor2): return roi.uid  ## Success.
64          return -1  ## Failure.
65          
66      def set_plot_all(self):
67          """Choose to plot every sensorgram."""
68 <        for ob in self.roi: ob.plottable = True
68 >        for roi in self.roi: roi.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
73 >        for roi in self.roi: roi.plottable = False
74          for i in ilist: self.roi[i].plottable = True
75 <    
76 <    ## A pyplot feature for testing purposes.
77 <    def plot(self):
53 <        """Show plot of the selected sensorgrams."""
54 <        plt.clf()
55 <        plt.title('SPR Data plotted %s' % date.today().isoformat())
56 <        plt.xlabel('Time (s)')
57 <        plt.ylabel('SPR Response')
58 <        plt.grid(True)
59 <        ## Plot traces.
60 <        for ob in self.roi:
61 <            if (ob.plottable==True):
62 <                mylabel = "%i:%s" % (ob.index,ob.name)
63 <                plt.plot(ob.time, ob.value, label=mylabel)
64 <        plt.legend(loc='best')
65 <        plt.show()
66 <    ### End of BiosensorArray class definition.
75 >        return
76 >        
77 >    """End of BiosensorArray class definition."""
78  
79  
80   class RegOfInterest(object):
81 <    """This Region Of Interest class can hold one SPR sensorgram."""
81 >    """
82 >    This Region Of Interest class can hold one SPR sensorgram.
83 >    
84 >    =========== =============== =============================================
85 >    Property    Type            Description
86 >    ----------- --------------- ---------------------------------------------
87 >    uid         integer         Unique ID integer. Never changes.
88 >    index       integer         Changes if ba size changes (add/remove rois).
89 >    time        nparray         Usually seconds.
90 >    value       nparray         Arbitrary units.
91 >    dpoints     integer         Can use for bounds checking.
92 >    name        string          Name of ROI.
93 >    desc        string          Description of ROI
94 >    
95 >    gridx       integer         Can be Block number from GAL file.  
96 >    gridy       integer         Unused?
97 >    spotx       integer         ROI column number.
98 >    spoty       integer         ROI row number.
99 >    bgroi       list of integer One or more background ROIs.
100 >    calibM      float           Slope used for calibration
101 >    calibB      float           Intercept used for calibration.
102 >    plottable   boolean         Whether to plot
103 >    
104 >    injconc     list of float   One or more analyte concentrations.
105 >    injstart    list of float   One or more injection start times.
106 >    injstop     list of float   One or more injection start times.
107 >    injrind     list of float   One or more expected refractive index jumps.
108 >    
109 >    flow        float           Flowrate of injection.
110 >    model       ref to funct    Model describing this ROI.
111 >    params      dict of dict    Parameters for this model.
112 >    =========== =============== =============================================
113 >    """
114 >    
115      def __init__(self, i, datapoint_size):
116          """
117          Each ROI in a list needs a unique ID number which will be i+1.
# Line 95 | Line 139
139          self.injstop = [0.0]     ## One or more injection start times.
140          self.injrind = [0.0]     ## One or more expected refractive index jumps.
141          self.flow = 0            ## Flowrate of injection.
142 +        ## Curve fitting information.  Model and model parameters.
143 +        ## Example model is reference to function like data=simple1to1(times,params)
144 +        ## Example params = {'Rmax': {'value':1, 'min':0, 'max':10, 'fixed':'float'} }
145 +        self.model = None    ## Model describing this roi. Reference to a function.
146 +        self.params = []     ## Parameters for this model. A dictionary of dictionaries.
147          
148      def time2dp(self, t):
149          """Find datapoint closest to given time."""
150 <        pos2 = self.time.searchsorted(t)  ## Time point just after t.
151 <        pos1 = max(pos2-1,0)
150 >        pos2 = self.time.searchsorted(t)    ## Time point just after t.
151 >        pos2 = min(pos2, len(self.time)-1)  ## Avoid indexing error.
152 >        pos1 = max(pos2-1,0)                ## Time point just before t.
153          t2 = abs(self.time[pos2] - t)
154          t1 = abs(self.time[pos1] - t)
155 +        ## Decide if time point just before or just after is closer.
156          if (t2<t1):
157              return pos2
158          else:
159              return pos1
160 <        
161 <    ## End of RegOfInterest definition.
160 >            
161 >    def time2val(self, t1, t2):
162 >        """Return list of SPR values between t1 and t2"""
163 >        dp1, dp2 = self.time2dp(t1), self.time2dp(t2)
164 >        return [self.value[i] for i in range(dp1, dp2)]
165 >    
166 >    """End of RegOfInterest definition."""
167  
168  
113 ## Here are a few lines to test this class.
114 if __name__ == '__main__':
115    print "Starting demo..."
116    print "Test plotting..."
117    x = BiosensorArray(10,10)
118    x.roi[0].time = np.arange(10)
119    x.roi[0].value = np.arange(10)**2
120    x.roi[1].time = np.arange(10)
121    x.roi[1].value = np.arange(10)**1.5
122    x.roi[9].time = np.arange(10)
123    x.roi[9].value = np.arange(10)**1
124    #x.set_plot_all()
125    x.set_plot_list([0,1,9])
126    x.plot()
127    print "Test xy2uid... 9 =",
128    x.roi[9].gridx = 2
129    print x.xy2uid(2,0,0,0)
130    print "Test time2dp... 5.6 =>",
131    print x.roi[9].time2dp(5.6)
132    print "Demo finished."
133    
134    
135 ################################# End of module #################################
169 + ################################# End of module #################################

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