osprai/trunk/ba_class.py

"""
ba: Biosensor Array class for storing SPRI data.
Christopher Lausted, Institute for Systems Biology, 
Yuhang Wan, OSPRAI developers
Last modified on 100517 (yymmdd)

Examples:
#ba1 = BiosensorArray(800,1500)     ## Allocate object with 800 spots of 1500 time points.
#ba1.roi[799].time[1499] = 7502.1   ## Set time in seconds.
#ba1.roi[799].value[1499] = 0.50    ## Set SPR reflectance signal. 
#ba1.roi[799].name = "anti-IgG"     ## Set name of microarray feature.
"""
__version__ = "100517"

## Import libraries.
import numpy as np
#import matplotlib.pyplot as plt
from datetime import date


class BiosensorArray(object):
    """
    The Biosensor Array class holds all ROIs (spots)
    from an SPRI microarray run.
    
    Property    Type            Description
    --------    --------------  ---------------------------------------
    roi         list of object  List of RegOfInterest objects.
    rois        integer         Size of roi (Number of ROIs).
    dpoints     integer         Number of datapoints in each ROI.
    primarydatafiles            List of file names.
    comments    list of string  List of comments regarding experiments.
    """
    
    def __init__(self, roi_size, datapoint_size):
        """This object is dimensioned upon initialization.""" ## Might improve speed.
        ## Use a list comprehension to dimension list of classes.
        self.roi = [RegOfInterest(i,datapoint_size) for i in range(roi_size)] 
        ## Remember the dimensions for quick bounds-checking later.
        self.rois = roi_size
        self.dpoints = datapoint_size
        ## Use these to keep track of laboratory notes.
        self.primarydatafiles = [""]  ## Like "spritdata.txt"
        self.comments = [""]          ## Like "Antibody data from 1 Jan 2010"
        
    def xy2uid(self, gx, gy, x, y):
        """Given roi coordinates, find corresponding uid (index)."""
        coor1 = (gx, gy, x, y)
        for ob in self.roi:
            coor2 = (ob.gridx, ob.gridy, ob.spotx, ob.spoty)
            if (coor1==coor2): return ob.uid  ## Success.
        return -1  ## Failure.
        
    def set_plot_all(self):
        """Choose to plot every sensorgram."""
        for ob in self.roi: ob.plottable = True
        
    def set_plot_list(self, ilist):
        """Choose a list of sensorgrams to plot"""
        for ob in self.roi: ob.plottable = False
        for i in ilist: self.roi[i].plottable = True
    
    ## A pyplot feature for testing purposes.
    def plot(self):
        """Show plot of the selected sensorgrams."""
        plt.clf()
        plt.title('SPR Data plotted %s' % date.today().isoformat())
        plt.xlabel('Time (s)')
        plt.ylabel('SPR Response')
        plt.grid(True)
        ## Plot traces.
        for ob in self.roi:
            if (ob.plottable==True):
                mylabel = "%i:%s" % (ob.index,ob.name)
                plt.plot(ob.time, ob.value, label=mylabel)
        plt.legend(loc='best')
        plt.show()
    ### End of BiosensorArray class definition.


class RegOfInterest(object):
    """
    This Region Of Interest class can hold one SPR sensorgram.
    
    Property    Type            Description
    --------    --------------  ---------------------------------------------
    uid         integer         Unique ID integer. Never changes.
    index       integer         Changes if ba size changes (add/remove rois).
    time        nparray         Usually seconds.
    value       nparray         Arbitrary units.
    dpoints     integer         Can use for bounds checking.
    name        string          Name of ROI.
    desc        string          Description of ROI
    
    gridx       integer         Can be Block number from GAL file.  
    gridy       integer         Unused?
    spotx       integer         ROI column number.
    spoty       integer         ROI row number.
    bgroi       list of integer One or more background ROIs.
    calibM      float           Slope used for calibration
    calibB      float           Intercept used for calibration.
    plottable   boolean         Whether to plot
    
    injconc     list of float   One or more analyte concentrations.
    injstart    list of float   One or more injection start times.
    injstop     list of float   One or more injection start times.
    injrind     list of float   One or more expected refractive index jumps.
    
    flow        float           Flowrate of injection.
    model       ref to funct    Model describing this ROI. 
    params      dict of dict    Parameters for this model. 
    """
    
    def __init__(self, i, datapoint_size):
        """
        Each ROI in a list needs a unique ID number which will be i+1.
        The time and value arrays must be allocated using datapoint_size.
        """
        self.uid = i+1            ## Unique ID integer. Never changes.
        self.index = i            ## Changes if ba size changes (add/remove rois).
        self.time = np.zeros(datapoint_size, dtype=float)  ## Usually seconds.
        self.value = np.zeros(datapoint_size, dtype=float) ## Arbitrary units.
        self.dpoints = datapoint_size  ## Can use for bounds checking.
        ## Useful optional information. Usually from GAL or Key files.
        self.name = "Spot%i" % (i+1)
        self.desc = "Description"
        self.gridx = 0            ## Can be Block number from GAL file.  
        self.gridy = 0            ## Unused?
        self.spotx = 0            ## ROI column number.
        self.spoty = 0            ## ROI row number.
        self.bgroi = [0]          ## One or more background ROIs.
        self.calibM = 1           ## Slope used for calibration
        self.calibB = 0           ## Intercept used for calibration.
        self.plottable = True     ## Whether to plot
        ## Optional injection information. Usually from Clamp or ICM Method files.
        self.injconc = [0.0]     ## One or more analyte concentrations.
        self.injstart = [0.0]    ## One or more injection start times.
        self.injstop = [0.0]     ## One or more injection start times.
        self.injrind = [0.0]     ## One or more expected refractive index jumps.
        self.flow = 0            ## Flowrate of injection.
        ## Curve fitting information.  Model and model parameters.
        ## Example model is reference to function like data=simple1to1(times,params)
        ## Example params = {'Rmax': {'value':1, 'min':0, 'max':10, 'fixed':'float'} } 
        self.model = None    ## Model describing this roi. Reference to a function.
        self.params = []     ## Parameters for this model. A dictionary of dictionaries.
        
    def time2dp(self, t):
        """Find datapoint closest to given time."""
        pos2 = self.time.searchsorted(t)    ## Time point just after t.
        pos2 = min(pos2, len(self.time)-1)  ## Avoid indexing error.
        pos1 = max(pos2-1,0)                ## Time point just before t.
        t2 = abs(self.time[pos2] - t)
        t1 = abs(self.time[pos1] - t)
        ## Decide if time point just before or just after is closer.
        if (t2<t1): 
            return pos2
        else: 
            return pos1
            
    def time2val(self, t1, t2):
        """Return list of SPR values between t1 and t2"""
        dp1, dp2 = self.time2dp(t1), self.time2dp(t2)
        return [self.value[i] for i in range(dp1, dp2)]
    
    ## End of RegOfInterest definition.

'''
## Here are a few lines to test this class.
if __name__ == '__main__':
    print "Starting demo..."
    print "Test plotting..."
    x = BiosensorArray(10,10)
    x.roi[0].time = np.arange(10)
    x.roi[0].value = np.arange(10)**2
    x.roi[1].time = np.arange(10)
    x.roi[1].value = np.arange(10)**1.5
    x.roi[9].time = np.arange(10)
    x.roi[9].value = np.arange(10)**1
    #x.set_plot_all()
    x.set_plot_list([0,1,9])
    x.plot()
    print "Test xy2uid... 9 =",
    x.roi[9].gridx = 2
    print x.xy2uid(2,0,0,0)
    print "Test time2dp... 5.6 =>",
    print x.roi[9].time2dp(5.6)
    print "Demo finished."
'''
    
    
################################# End of module #################################
Revision:	28
Committed:	Wed May 19 06:06:07 2010 UTC (9 years, 6 months ago) by clausted
File size:	8162 byte(s)
Log Message:	Changes to params dictionary. Valid values for 'fixed' are 'fixed' 'float' or an integer. True and False are no longer acceptable. Now mutli-ROI curve fitting seems to work!
Line	File contents
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.
12	"""
13	__version__ = "100517"
14
15	## Import libraries.
16	import numpy as np
17	#import matplotlib.pyplot as plt
18	from datetime import date
19
20
21	class BiosensorArray(object):
22	"""
23	The Biosensor Array class holds all ROIs (spots)
24	from an SPRI microarray run.
25
26	Property Type Description
27	-------- -------------- ---------------------------------------
28	roi list of object List of RegOfInterest objects.
29	rois integer Size of roi (Number of ROIs).
30	dpoints integer Number of datapoints in each ROI.
31	primarydatafiles List of file names.
32	comments list of string List of comments regarding experiments.
33	"""
34
35	def __init__(self, roi_size, datapoint_size):
36	"""This object is dimensioned upon initialization.""" ## Might improve speed.
37	## Use a list comprehension to dimension list of classes.
38	self.roi = [RegOfInterest(i,datapoint_size) for i in range(roi_size)]
39	## Remember the dimensions for quick bounds-checking later.
40	self.rois = roi_size
41	self.dpoints = datapoint_size
42	## Use these to keep track of laboratory notes.
43	self.primarydatafiles = [""] ## Like "spritdata.txt"
44	self.comments = [""] ## Like "Antibody data from 1 Jan 2010"
45
46	def xy2uid(self, gx, gy, x, y):
47	"""Given roi coordinates, find corresponding uid (index)."""
48	coor1 = (gx, gy, x, y)
49	for ob in self.roi:
50	coor2 = (ob.gridx, ob.gridy, ob.spotx, ob.spoty)
51	if (coor1==coor2): return ob.uid ## Success.
52	return -1 ## Failure.
53
54	def set_plot_all(self):
55	"""Choose to plot every sensorgram."""
56	for ob in self.roi: ob.plottable = True
57
58	def set_plot_list(self, ilist):
59	"""Choose a list of sensorgrams to plot"""
60	for ob in self.roi: ob.plottable = False
61	for i in ilist: self.roi[i].plottable = True
62
63	## A pyplot feature for testing purposes.
64	def plot(self):
65	"""Show plot of the selected sensorgrams."""
66	plt.clf()
67	plt.title('SPR Data plotted %s' % date.today().isoformat())
68	plt.xlabel('Time (s)')
69	plt.ylabel('SPR Response')
70	plt.grid(True)
71	## Plot traces.
72	for ob in self.roi:
73	if (ob.plottable==True):
74	mylabel = "%i:%s" % (ob.index,ob.name)
75	plt.plot(ob.time, ob.value, label=mylabel)
76	plt.legend(loc='best')
77	plt.show()
78	### End of BiosensorArray class definition.
79
80
81	class RegOfInterest(object):
82	"""
83	This Region Of Interest class can hold one SPR sensorgram.
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	def __init__(self, i, datapoint_size):
115	"""
116	Each ROI in a list needs a unique ID number which will be i+1.
117	The time and value arrays must be allocated using datapoint_size.
118	"""
119	self.uid = i+1 ## Unique ID integer. Never changes.
120	self.index = i ## Changes if ba size changes (add/remove rois).
121	self.time = np.zeros(datapoint_size, dtype=float) ## Usually seconds.
122	self.value = np.zeros(datapoint_size, dtype=float) ## Arbitrary units.
123	self.dpoints = datapoint_size ## Can use for bounds checking.
124	## Useful optional information. Usually from GAL or Key files.
125	self.name = "Spot%i" % (i+1)
126	self.desc = "Description"
127	self.gridx = 0 ## Can be Block number from GAL file.
128	self.gridy = 0 ## Unused?
129	self.spotx = 0 ## ROI column number.
130	self.spoty = 0 ## ROI row number.
131	self.bgroi = [0] ## One or more background ROIs.
132	self.calibM = 1 ## Slope used for calibration
133	self.calibB = 0 ## Intercept used for calibration.
134	self.plottable = True ## Whether to plot
135	## Optional injection information. Usually from Clamp or ICM Method files.
136	self.injconc = [0.0] ## One or more analyte concentrations.
137	self.injstart = [0.0] ## One or more injection start times.
138	self.injstop = [0.0] ## One or more injection start times.
139	self.injrind = [0.0] ## One or more expected refractive index jumps.
140	self.flow = 0 ## Flowrate of injection.
141	## Curve fitting information. Model and model parameters.
142	## Example model is reference to function like data=simple1to1(times,params)
143	## Example params = {'Rmax': {'value':1, 'min':0, 'max':10, 'fixed':'float'} }
144	self.model = None ## Model describing this roi. Reference to a function.
145	self.params = [] ## Parameters for this model. A dictionary of dictionaries.
146
147	def time2dp(self, t):
148	"""Find datapoint closest to given time."""
149	pos2 = self.time.searchsorted(t) ## Time point just after t.
150	pos2 = min(pos2, len(self.time)-1) ## Avoid indexing error.
151	pos1 = max(pos2-1,0) ## Time point just before t.
152	t2 = abs(self.time[pos2] - t)
153	t1 = abs(self.time[pos1] - t)
154	## Decide if time point just before or just after is closer.
155	if (t2<t1):
156	return pos2
157	else:
158	return pos1
159
160	def time2val(self, t1, t2):
161	"""Return list of SPR values between t1 and t2"""
162	dp1, dp2 = self.time2dp(t1), self.time2dp(t2)
163	return [self.value[i] for i in range(dp1, dp2)]
164
165	## End of RegOfInterest definition.
166
167	'''
168	## Here are a few lines to test this class.
169	if __name__ == '__main__':
170	print "Starting demo..."
171	print "Test plotting..."
172	x = BiosensorArray(10,10)
173	x.roi[0].time = np.arange(10)
174	x.roi[0].value = np.arange(10)**2
175	x.roi[1].time = np.arange(10)
176	x.roi[1].value = np.arange(10)**1.5
177	x.roi[9].time = np.arange(10)
178	x.roi[9].value = np.arange(10)**1
179	#x.set_plot_all()
180	x.set_plot_list([0,1,9])
181	x.plot()
182	print "Test xy2uid... 9 =",
183	x.roi[9].gridx = 2
184	print x.xy2uid(2,0,0,0)
185	print "Test time2dp... 5.6 =>",
186	print x.roi[9].time2dp(5.6)
187	print "Demo finished."
188	'''
189
190
191	################################# End of module #################################