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netpyne/analysis/__init__.py

@@ -7,6 +7,7 @@
 from .tools import getInclude, plotData, saveData, loadData
 from .utils import exception, _showFigure, _saveFigData, getCellsInclude, getCellsIncludeTags, _roundFigures, _smooth1d, syncMeasure, invertDictMapping, checkAvailablePlots
 
+from netpyne.logger import logger
 # Import connectivity-related functions
 from .network import plotConn, _plotConnCalculateFromSim, _plotConnCalculateFromFile, plot2Dnet, plotShape, calculateDisynaptic, plot2Dfiring
 
@@ -33,7 +34,7 @@
 try:
     from .interactive import iplotDipole, iplotDipoleSpectrogram, iplotDipolePSD, iplotRaster, iplotSpikeHist, iplotRatePSD, iplotTraces, iplotLFP, iplotConn, iplotRxDConcentration, iplot2Dnet, iplotSpikeStats
 except:
-    print('Warning: could not import interactive plotting functions; make sure the "bokeh" package is installed.')
+    logger.warning('Could not import interactive plotting functions; make sure the "bokeh" package is installed.')
 
 # Import CSD-related functions
 from .csd import getCSD, plotCSD

netpyne/analysis/csd.py

@@ -3,7 +3,6 @@
 
 """
 
-from __future__ import print_function
 from __future__ import division
 from __future__ import unicode_literals
 from __future__ import absolute_import
@@ -31,7 +30,7 @@
 from scipy.signal import cheb2ord, cheby2, convolve, get_window, iirfilter, remez, decimate
 from .filter import lowpass,bandpass
 from .utils import exception, _saveFigData 
-
+from netpyne.logger import logger
 
 def getbandpass(lfps, sampr, minf=0.05, maxf=300):
     """
@@ -320,7 +319,7 @@ def getCSD(LFP_input_data=None, LFP_input_file=None, sampr=None, dt=None, spacin
             sim.allSimData['CSD']['CSD_data'] = CSD_data
             sim.allSimData['CSD']['CSD_data_noBandpass'] = CSD_data_noBandpass 
         except:
-            print('NOTE: No sim.allSimData construct available to store CSD data.')
+            logger.warning('No sim.allSimData construct available to store CSD data.')
 
     # return CSD_data or all data
     if getAllData is True:
@@ -400,8 +399,8 @@ def plotCSD(CSD_data=None, LFP_input_data=None, overlay=None, timeRange=None, sa
 
     """
 
-    print('Plotting CSD... ')
-  
+    logger.info('Plotting CSD...')
+
     # DEFAULT -- CONDITION 1 : GET CSD DATA FROM SIM
     if CSD_data is None:
 
@@ -439,24 +438,24 @@ def plotCSD(CSD_data=None, LFP_input_data=None, overlay=None, timeRange=None, sa
     # CONDITION 2 : ARBITRARY CSD DATA 
     elif CSD_data is not None:
         if timeRange is None:
-            print('MUST PROVIDE TIME RANGE in ms')
+            logger.warning('Must provide time range in in ms')
         else:
-            print('timeRange = ' + str(timeRange))
+            logger.info('timeRange = ' + str(timeRange))
 
         if dt is None:
-            print('MUST PROVIDE dt in ms')
+            logger.warning('Must provide dt in ms')
         else:
-            print('dt = ' + str(dt)) # batch0['simConfig']['recordStep']
+            logger.info('dt = ' + str(dt)) # batch0['simConfig']['recordStep']
 
         if spacing_um is None:
-            print('MUST PROVIDE SPACING BETWEEN ELECTRODES in MICRONS')
+            logger.warning('Must provide spacing between electrodes in microns')
         else:
-            print('spacing_um = ' + str(spacing_um))
+            logger.info('spacing_um = ' + str(spacing_um))
 
         if ymax is None:
-            print('MUST PROVIDE YMAX (MAX DEPTH) in MICRONS')
+            logger.warning('Must provide ymax (max depth) in microns')
         else:
-            print('ymax = ' + str(ymax))
+            logger.info('ymax = ' + str(ymax))
 
         tt = np.arange(timeRange[0], timeRange[1], dt)
         LFP_data = np.array(LFP_input_data)[int(timeRange[0]/dt):int(timeRange[1]/dt),:]
@@ -538,7 +537,7 @@ def plotCSD(CSD_data=None, LFP_input_data=None, overlay=None, timeRange=None, sa
                 subaxs[chan].plot(X, LFP_data[:,chan], color='gray', linewidth=0.3)
 
     else:
-        print('No data being overlaid')
+        logger.info('No data being overlaid')
         axs[0].set_title('Current Source Density (CSD)', fontsize=fontSize)
 
 
@@ -550,7 +549,7 @@ def plotCSD(CSD_data=None, LFP_input_data=None, overlay=None, timeRange=None, sa
 
     if layer_lines: 
         if layer_bounds is None:
-            print('No layer boundaries given')
+            logger.info('No layer boundaries given')
         else:
             layerKeys = []
         for i in layer_bounds.keys():

netpyne/analysis/filter.py

@@ -21,7 +21,6 @@
 
 """
 
-from __future__ import print_function
 from __future__ import division
 from __future__ import unicode_literals
 from __future__ import absolute_import

netpyne/analysis/info.py

@@ -3,7 +3,6 @@
 
 """
 
-from __future__ import print_function
 from __future__ import division
 from __future__ import unicode_literals
 from __future__ import absolute_import
@@ -22,7 +21,7 @@
     import matplotlib.pyplot as plt
 import numpy as np
 from .utils import exception, _saveFigData, _showFigure, getCellsInclude
-
+from netpyne.logger import logger
 
 # -------------------------------------------------------------------------------------------------------------------
 ## Calculate normalized transfer entropy
@@ -102,13 +101,13 @@ def nTE(cells1=[], cells2=[], spks1=None, spks2=None, timeRange=None, binSize=20
 
     if 'nte' not in dir(h):
         try:
-            print(' Warning: support/nte.mod not compiled; attempting to compile from %s via "nrnivmodl support"'%(root))
+            logger.warning('support/nte.mod not compiled; attempting to compile from %s via "nrnivmodl support"'%(root))
             os.system('cd ' + root + '; nrnivmodl support')
             from neuron import load_mechanisms
             load_mechanisms(root)
-            print(' Compilation of support folder mod files successful')
+            logger.info('Compilation of support folder mod files successful')
         except:
-            print(' Error compiling support folder mod files')
+            logger.warning('Error compiling support folder mod files')
             return
 
     h.load_file(root+'/support/nte.hoc') # nTE code (also requires support/net.mod)
@@ -376,7 +375,7 @@ def plotGranger(cells1=None, cells2=None, spks1=None, spks2=None, label1=None, l
         try:
             from statsmodels.tsa.stattools import grangercausalitytests as gt
         except:
-            print('To test Granger results please install the statsmodel package: "pip install statsmodel"')
+            logger.warning('To test Granger results please install the statsmodel package: "pip install statsmodel"')
             exit()
 
         tests = gt(np.array([histoCount1, histoCount2]).T, maxlag=10)

netpyne/analysis/interactive.py

@@ -4,7 +4,6 @@
 """
 
 from __future__ import unicode_literals
-from __future__ import print_function
 from __future__ import division
 from __future__ import absolute_import
 
@@ -32,6 +31,7 @@
 from bokeh.palettes import Viridis256
 from bokeh.models import HoverTool
 
+from netpyne.logger import logger
 
 def applyTheme(kwargs):
     theme = None
@@ -171,7 +171,7 @@ def iplotRaster(include=['allCells'], timeRange=None, maxSpikes=1e8, orderBy='gi
     from bokeh.colors import RGB
     from bokeh.models.annotations import Title
 
-    print('Plotting interactive raster ...')
+    logger.info('Plotting interactive raster...')
 
     theme = applyTheme(kwargs)
 
@@ -218,7 +218,7 @@ def iplotRaster(include=['allCells'], timeRange=None, maxSpikes=1e8, orderBy='gi
             sel, spkts, spkgids = getSpktSpkid(cellGids=[] if include == ['allCells'] else cellGids, timeRange=timeRange)
         except:
             import sys
-            print((sys.exc_info()))
+            logger.warning(sys.exc_info())
             spkgids, spkts = [], []
             sel = pd.DataFrame(columns=['spkt', 'spkid'])
         sel['spkgidColor'] = sel['spkid'].map(gidColors)
@@ -252,14 +252,13 @@ def iplotRaster(include=['allCells'], timeRange=None, maxSpikes=1e8, orderBy='gi
             numNetStims += 1
         else:
             pass
-            #print netStimLabel+' produced no spikes'
     if len(cellGids)>0 and numNetStims:
         ylabelText = ylabelText + ' and NetStims (at the end)'
     elif numNetStims:
         ylabelText = ylabelText + 'NetStims'
 
     if numCellSpks+numNetStims == 0:
-        print('No spikes available to plot raster')
+        logger.warning('No spikes available to plot raster')
         return None
 
     # Time Range
@@ -272,7 +271,7 @@ def iplotRaster(include=['allCells'], timeRange=None, maxSpikes=1e8, orderBy='gi
 
     # Limit to max spikes
     if (len(sel)>maxSpikes):
-        print(('  Showing only the first %i out of %i spikes' % (maxSpikes, len(sel)))) # Limit num of spikes
+        logger.info('  Showing only the first %i out of %i spikes' % (maxSpikes, len(sel))) # Limit num of spikes
         if numNetStims: # sort first if have netStims
             sel = sel.sort_values(by='spkt')
         sel = sel.iloc[:maxSpikes]
@@ -321,7 +320,6 @@ def iplotRaster(include=['allCells'], timeRange=None, maxSpikes=1e8, orderBy='gi
     if syncLines:
         for spkt in sel['spkt'].tolist():
             fig.line((spkt, spkt), (0, len(cells)+numNetStims), color='red', line_width=2)
-        print(syncMeasure())
         t.text = 'cells=%i  syns/cell=%0.1f  rate=%0.1f Hz  sync=%0.2f' % (numCells,connsPerCell,firingRate,syncMeasure())
     else:
         t.text = 'cells=%i  syns/cell=%0.1f  rate=%0.1f Hz' % (numCells,connsPerCell,firingRate)
@@ -967,7 +965,7 @@ def iplotSpikeHist(include = ['allCells', 'eachPop'], legendLabels = [], timeRan
     from bokeh.models import Legend
     from bokeh.colors import RGB
 
-    print('Plotting interactive spike histogram...')
+    logger.info('Plotting interactive spike histogram...')
 
     theme = applyTheme(kwargs)
 
@@ -1085,7 +1083,7 @@ def iplotSpikeHist(include = ['allCells', 'eachPop'], legendLabels = [], timeRan
         fig.legend.click_policy='hide'
         fig.legend.location='top_right'
 
-    print(figs)
+    logger.info(figs)
     plot_layout = gridplot(figs, ncols=1, merge_tools=False, sizing_mode='stretch_both')
     html = file_html(plot_layout, CDN, title="Spike Histogram", theme=theme)
 
@@ -1191,7 +1189,7 @@ def iplotRatePSD(include=['allCells', 'eachPop'], timeRange=None, binSize=5, max
     from bokeh.colors import RGB
     from bokeh.models import Legend
 
-    print('Plotting interactive firing rate power spectral density (PSD) ...')
+    logger.info('Plotting interactive firing rate power spectral density (PSD) ...')
 
     theme = applyTheme(kwargs)
 
@@ -1407,7 +1405,7 @@ def iplotTraces(include=None, timeRange=None, overlay=False, oneFigPer='cell', r
     from bokeh.models import Legend
     from bokeh.colors import RGB
 
-    print('Plotting interactive recorded cell traces per', oneFigPer)
+    logger.info('Plotting interactive recorded cell traces per ' + oneFigPer)
 
     theme = applyTheme(kwargs)
 
@@ -1736,7 +1734,7 @@ def iplotLFP(electrodes=['avg', 'all'], plots=['timeSeries', 'PSD', 'spectrogram
     from bokeh.layouts import layout, column, row
     from bokeh.colors import RGB
 
-    print('Plotting interactive LFP ...')
+    logger.info('Plotting interactive LFP ...')
 
     html = None
     theme = applyTheme(kwargs)
@@ -2137,7 +2135,7 @@ def iplotConn(includePre=['all'], includePost=['all'], feature='strength', order
     from bokeh.layouts import layout
     from bokeh.colors import RGB
 
-    print('Plotting interactive connectivity matrix...')
+    logger.info('Plotting interactive connectivity matrix...')
 
     theme = applyTheme(kwargs)
 
@@ -2148,7 +2146,7 @@ def iplotConn(includePre=['all'], includePost=['all'], feature='strength', order
 
 
     if connMatrix is None:
-        print("  Error calculating connMatrix in iplotConn()")
+        logger.info("  Error calculating connMatrix in iplotConn()")
         return None
 
     # TODO: set plot font size in Bokeh
@@ -2253,11 +2251,11 @@ def iplotConn(includePre=['all'], includePost=['all'], feature='strength', order
             fig.yaxis.axis_label = feature
 
         elif groupBy == 'cell':
-            print('  Error: plotConn graphType="bar" with groupBy="cell" not yet implemented')
+            logger.warning('  Error: plotConn graphType="bar" with groupBy="cell" not yet implemented')
             return None
 
     elif graphType == 'pie':
-        print('  Error: plotConn graphType="pie" not yet implemented')
+        logger.warning('  Error: plotConn graphType="pie" not yet implemented')
         return None
 
     plot_layout = layout([fig], sizing_mode='stretch_both')
@@ -2375,7 +2373,7 @@ def iplot2Dnet(include=['allCells'], view='xy', showConns=True, popColors=None,
     from bokeh.colors import RGB
     from bokeh.models.annotations import Title
 
-    print('Plotting interactive 2D representation of network cell locations and connections...')
+    logger.info('Plotting interactive 2D representation of network cell locations and connections...')
 
     theme = applyTheme(kwargs)
 
@@ -2393,7 +2391,7 @@ def iplot2Dnet(include=['allCells'], view='xy', showConns=True, popColors=None,
         ycoord = 'z'
 
     if tagsFile:
-        print('Loading tags file...')
+        logger.info('Loading tags file...')
         import json
         with open(tagsFile, 'r') as fileObj: tagsTmp = json.load(fileObj)['tags']
         tagsFormat = tagsTmp.pop('format', [])
@@ -2407,8 +2405,8 @@ def iplot2Dnet(include=['allCells'], view='xy', showConns=True, popColors=None,
         yIndex = tagsFormat.index('y') if 'y' in tagsFormat else missing.append('y')
         zIndex = tagsFormat.index('z') if 'z' in tagsFormat else missing.append('z')
         if len(missing) > 0:
-            print("Missing:")
-            print(missing)
+            logger.info("Missing:")
+            logger.info(missing)
             return None, None, None
 
         # find pre and post cells
@@ -2429,7 +2427,7 @@ def iplot2Dnet(include=['allCells'], view='xy', showConns=True, popColors=None,
             elif ycoord == 'z':
                 posY = [tags[gid][zIndex] for gid in cellGids]  # get all y positions
         else:
-            print('Error loading tags from file')
+            logger.warning('Error loading tags from file')
             return None
 
     else:
@@ -2580,7 +2578,7 @@ def iplotRxDConcentration(speciesLabel, regionLabel, plane='xy', saveFig=None, s
     from bokeh.transform import linear_cmap
     from bokeh.models import ColorBar
 
-    print('Plotting interactive RxD concentration ...')
+    logger.info('Plotting interactive RxD concentration ...')
 
     theme = applyTheme(kwargs)
 
@@ -2790,7 +2788,7 @@ def iplotSpikeStats(include=['eachPop', 'allCells'], statDataIn={}, timeRange=No
     from bokeh.palettes import Spectral6
     from bokeh.models.mappers import CategoricalColorMapper
 
-    print('Plotting interactive spike statistics ...')
+    logger.info('Plotting interactive spike statistics ...')
 
     TOOLS = "pan,wheel_zoom,box_zoom,reset,save,box_select"
 
@@ -2887,7 +2885,7 @@ def iplotSpikeStats(include=['eachPop', 'allCells'], statDataIn={}, timeRange=No
                     try:
                         import pyspike
                     except:
-                        print("Error: plotSpikeStats() requires the PySpike python package \
+                        logger.warning("Error: plotSpikeStats() requires the PySpike python package \
                             to calculate synchrony (try: pip install pyspike)")
                         return 0