from __future__ import print_function,division import logging as log log.basicConfig(level=log.INFO) import numpy as np np.seterr(all='ignore') import os import glob import pathlib import re from . import storage as storage try: import matplotlib.pyplot as plt except ImportError: log.warn("Can't import matplotlib !") _time_regex = re.compile( "(-?\d+\.?\d*(?:ps|ns|us|ms)?)") _timeInStr_regex = re.compile("_(-?\d+\.?\d*(?:ps|ns|us|ms)?)") def getFiles(folder,basename="*.edf*",nFiles=None): files = glob.glob(folder + "/" + basename) files.sort() if nFiles is not None: files = files[:nFiles] return files def getEdfFiles(folder,**kw): return getFiles(folder,basename="*.edf*",**kw) def getDelayFromString(string) : match = _timeInStr_regex_regex.search(string) return match and match.group(1) or None _time_regex = re.compile("(-?\d+\.?\d*)((?:s|fs|ms|ns|ps|us)?)") def strToTime(delay) : _time2value = dict( fs = 1e-15, ps = 1e-12, ns = 1e-9, us = 1e-6, ms = 1e-3, s = 1) match = _time_regex.search(delay) if match: n,t = float(match.group(1)),match.group(2) value = _time2value.get(t,1) return n*value else: return None def timeToStr(delay,fmt="%+.0f"): a_delay = abs(delay) if a_delay >= 1: ret = fmt % delay + "s" elif 1e-3 <= a_delay < 1: ret = fmt % (delay*1e3) + "ms" elif 1e-6 <= a_delay < 1e-3: ret = fmt % (delay*1e6) + "us" elif 1e-9 <= a_delay < 1e-6: ret = fmt % (delay*1e9) + "ns" elif 1e-12 <= a_delay < 1e-9: ret = fmt % (delay*1e12) + "ps" elif 1e-15 <= a_delay < 1e-12: ret = fmt % (delay*1e12) + "fs" elif 1e-18 <= a_delay < 1e-15: ret = fmt % (delay*1e12) + "as" else: ret = str(delay) +"s" return ret def removeExt(fname): """ special remove extension meant to work with compressed files.edf and .edf.gz files """ if fname[-3:] == ".gz": fname = fname[-3:] return os.path.splitext(fname)[0] def getBasename(fname): return removeExt(os.path.basename(fname)); def plotdata(q,data,x=None,plot=True,showTrend=True,title=None,clim='auto'): if not (plot or showTrend): return if x is None: x = np.arange(data.shape[0]) if clim == 'auto': clim = np.nanpercentile(data,(1.5,98.5)) one_plot = showTrend or plot two_plot = showTrend and plot if one_plot and not two_plot: fig,ax = plt.subplots(1,1) if two_plot: fig,ax = plt.subplots(1,2,sharey=True) ax = np.atleast_1d(ax) if showTrend: plt.sca(ax[0]) plt.pcolormesh(x,q,data.T) plt.xlabel("image number, 0 being older") plt.ylabel(r"q ($\AA^{-1}$)") plt.clim( *clim ) if plot: if showTrend: ax[1].plot(data.mean(axis=0),q) else: ax[0].plot(q,data.mean(axis=0)) if (plot or showTrend) and title is not None: plt.title(title) def plotdiffs(q,diffs,t,select=None,err=None,absSignal=None,absSignalScale=10, showErr=False,cmap=plt.cm.jet): # this selection trick done in this way allows to keep the same colors when # subselecting (because I do not change the size of diffs) if select is not None: indices = range(*select.indices(t.shape[0])) else: indices = range(len(t)) lines = [] if absSignal is not None: line = plt.plot(q,absSignal/absSignalScale, color='k',label="absSignal/%s"%str(absSignalScale))[0] lines.append(line) for idiff in indices: color = cmap(idiff/(len(diffs)-1)) label = timeToStr(t[idiff]) kw = dict( color = color, label = label ) if err is not None and showErr: line = plt.errorbar(q,diffs[idiff],err[idiff],**kw)[0] else: line = plt.plot(q,diffs[idiff],**kw)[0] lines.append(line) fig = plt.gcf() legend = plt.legend() plt.grid() plt.xlabel(r"q ($\AA^{-1}$)") # we will set up a dict mapping legend line to orig line, and enable # picking on the legend line lined = dict() for legline, origline in zip(legend.get_lines(), lines): legline.set_picker(5) # 5 pts tolerance lined[legline] = origline def onpick(event): # on the pick event, find the orig line corresponding to the # legend proxy line, and toggle the visibility legline = event.artist origline = lined[legline] vis = not origline.get_visible() origline.set_visible(vis) # Change the alpha on the line in the legend so we can see what lines # have been toggled if vis: legline.set_alpha(1.0) else: legline.set_alpha(0.2) fig = plt.gcf() fig.canvas.draw() fig.canvas.mpl_connect('pick_event', onpick) def saveTxt(fname,q,data,headerv=None,info=None,overwrite=True,columns=''): """ Write data to file 'fname' in text format. Inputs: q = x vector data = one or 2D array (first axis is q) info = dictionary (saved as '# key : value') or string headerv = vector to be used as header or string """ if os.path.exists(fname) and not overwrite: log.warn("File %s exists, returning",fname) return if isinstance(info,dict): header = [ "# %s : %s" %(k,str(v)) for (k,v) in info.items() ] header = "\n".join(header); # skip first #, will be added by np elif isinstance(info,str): header = info else: header = "" if isinstance(headerv,str): header += "\n%s" % headerv if data.ndim == 1: x = np.vstack( (q,data) ) elif data.ndim == 2: x = np.vstack( (q,data) ) if headerv is not None: headerv = np.concatenate(( (data.shape[1],),headerv)) x = np.hstack( (headerv[:,np.newaxis],x) ) if columns != '': s = "#" + " ".join( [str(c).center(12) for c in columns] ) header = header + "\n" + s if header != '' else s np.savetxt(fname,x.T,fmt="%+10.5e",header=header,comments='') def reshapeToBroadcast(what,ref): """ expand the 1d array 'what' to allow broadbasting to match multidimentional array 'ref'. The two arrays have to same the same dimensions along the first axis """ assert what.shape[0] == ref.shape[0] shape = [ref.shape[0],] + [1,]*(ref.ndim-1) return what.reshape(shape)