def tic(self, msg=None, **noteArgs):
if msg is not None:
if "methodName" not in noteArgs.keys():
noteArgs["methodName"] = self._methodName
if "end" not in noteArgs.keys(): noteArgs["end"] = ""
_msg.note(msg=msg, **noteArgs)
self.start = _time.time()
def note( self
, msg = None
, end = "\n"
, pre = False
):
self.timer.toc()
if self._reportEnabled:
if msg is None: msg = "done in " + str(np.round(self.timer.delta,decimals=6)) + " seconds."
if pre:
err.note( msg = msg
, methodName = self._methodName
, marginTop = 0
, marginBot = 0
, end = end
)
else:
print( msg, end = end )
self.timer.toc()
def __init__( self
, msg = None
, methodName = ""
, reportEnabled = True
, end = "\n"
):
self._methodName = methodName
self._reportEnabled = reportEnabled
self._oldFraction = 0.0
self._clockCounter = None
if self._reportEnabled and msg is not None:
err.note( msg = msg
, methodName = self._methodName
, marginTop = 0
, marginBot = 0
, end = end
)
self.timer = Timer()
def plot(self):
"""
.. py:method:: plot(self)
Generate a grid plot from the selected columns of the object's dataframe.
**Parameters**
None
**Returns**
None. However, this method causes side-effects by manipulating
the existing attributes of the object.
"""
# setup figure
scatterplotEnabled = self.scatterplot_kws is not None
lineplotEnabled = self.lineplot_kws is not None
distplotEnabled = self.distplot_kws is not None
kdeplotEnabled = (self.kdeplot_kws is not None) and (self.kdecorner
is not None)
lsplotEnabled = (scatterplotEnabled
or lineplotEnabled) and (self.lscorner is not None)
if self.set_kws == (): self.set_kws = {}
kdeUpperEnabled = False
kdeLowerEnabled = False
if kdeplotEnabled:
if self.kdecorner == "auto":
kdeLowerEnabled = True
elif isinstance(self.kdecorner, str):
if "upper" in self.kdecorner: kdeUpperEnabled = True
if "lower" in self.kdecorner: kdeLowerEnabled = True
else:
raise Exception(
"The input argument 'kdecorner' must be either,\n\n" +
" 'upper', 'lower', 'upper-lower', 'auto',\n\n" +
"or otherwise None.")
lsUpperEnabled = False
lsLowerEnabled = False
if lsplotEnabled:
if self.lscorner == "auto":
lsUpperEnabled = not kdeUpperEnabled
lsLowerEnabled = not kdeLowerEnabled
lsplotEnabled = lsLowerEnabled or lsUpperEnabled
elif isinstance(self.lscorner, str):
if "upper" in self.lscorner: lsUpperEnabled = True
if "lower" in self.lscorner:
lsLowerEnabled = True
if self.kdecorner == "auto":
kdeUpperEnabled = not lsUpperEnabled
kdeLowerEnabled = not lsLowerEnabled
kdeplotEnabled = kdeLowerEnabled or kdeUpperEnabled
else:
raise Exception(
"The input argument 'lscorner' must be either,\n\n" +
" 'upper', 'lower', 'upper-lower', 'auto',\n\n" +
"or otherwise None.")
elif kdeplotEnabled:
if self.kdecorner == "auto":
kdeUpperEnabled = True
kdeLowerEnabled = True
if self.kdeplot_kws == (): self.kdeplot_kws = {}
if isinstance(self.kdeplot_kws, dict):
#self.kdeplot_kws["cbar"]=True if lsplotEnabled==False else False
self.kdeplot_kws["cbar"] = False
if "cmap" not in self.kdeplot_kws.keys():
self.kdeplot_kws["cmap"] = "Blues"
if "alpha" not in self.kdeplot_kws.keys():
self.kdeplot_kws["alpha"] = 1
if "shade" not in self.kdeplot_kws.keys():
self.kdeplot_kws["shade"] = True
if "n_levels" not in self.kdeplot_kws.keys():
self.kdeplot_kws["n_levels"] = 100
if "shade_lowest" not in self.kdeplot_kws.keys():
self.kdeplot_kws["shade_lowest"] = True
elif kdeplotEnabled:
raise Exception(
"The input argument 'kdeplot_kws' must be None or a dictionary,\n"
+
"each (key,value) pair of which represents an (attribute,value)\n"
+ "of seaborn library's kdeplot() function.")
if self.distplot_kws == (): self.distplot_kws = {}
if isinstance(self.distplot_kws, dict):
if "kde" not in self.distplot_kws.keys():
self.distplot_kws["kde"] = False
if "hist_kws" not in self.distplot_kws.keys():
self.distplot_kws["hist_kws"] = {
"histtype": "stepfilled",
"linewidth": 1
}
elif distplotEnabled:
raise Exception(
"The input argument 'distplot_kws' must be None or a dictionary,\n"
+
"each (key,value) pair of which represents an (attribute,value)\n"
+ "of seaborn library's distplot() function.")
if self.lineplot_kws == (): self.lineplot_kws = {}
if isinstance(self.lineplot_kws, dict):
self.lineplot_kws["figure_kws"] = None
if "legend_kws" not in self.lineplot_kws.keys():
self.lineplot_kws["legend_kws"] = None
if "colorbar_kws" not in self.lineplot_kws.keys():
self.lineplot_kws["colorbar_kws"] = None
if "lc_kws" not in self.lineplot_kws.keys():
self.lineplot_kws["lc_kws"] = {"cmap": "winter"}
if "set_kws" not in self.lineplot_kws.keys():
self.lineplot_kws["set_kws"] = self.set_kws
if "ccolumns" not in self.lineplot_kws.keys():
if scatterplotEnabled:
self.lineplot_kws["ccolumns"] = None
else:
self.lineplot_kws["ccolumns"] = ()
if self.lineplot_kws["ccolumns"] is None:
if scatterplotEnabled:
if "plot_kws" in self.lineplot_kws.keys():
if "color" not in self.lineplot_kws["plot_kws"].keys():
self.lineplot_kws["plot_kws"]["color"] = "grey"
if "alpha" not in self.lineplot_kws["plot_kws"].keys():
self.lineplot_kws["plot_kws"]["alpha"] = 0.3
else:
self.lineplot_kws["plot_kws"] = {
"color": "grey",
"alpha": 0.3
}
else:
if "plot_kws" not in self.lineplot_kws.keys():
self.lineplot_kws["plot_kws"] = None
elif lineplotEnabled:
raise Exception(
"The input argument 'lineplot_kws' must be None or a dictionary,\n"
+
"each (key,value) pair of which represents an (attribute,value)\n"
+ "of ParaMonte library's LinePlot() class.")
if self.scatterplot_kws == (): self.scatterplot_kws = {}
if isinstance(self.scatterplot_kws, dict):
self.scatterplot_kws["figure_kws"] = None
if "legend_kws" not in self.scatterplot_kws.keys():
self.scatterplot_kws["legend_kws"] = None
if "colorbar_kws" not in self.scatterplot_kws.keys():
self.scatterplot_kws["colorbar_kws"] = None
if "set_kws" not in self.scatterplot_kws.keys():
self.scatterplot_kws["set_kws"] = self.set_kws
if "scatter_kws" in self.scatterplot_kws.keys():
if "s" not in self.scatterplot_kws["scatter_kws"].keys():
self.scatterplot_kws["scatter_kws"]["s"] = 3
if "cmap" not in self.scatterplot_kws["scatter_kws"].keys():
self.scatterplot_kws["scatter_kws"]["cmap"] = "winter"
if "alpha" not in self.scatterplot_kws["scatter_kws"].keys():
self.scatterplot_kws["scatter_kws"]["alpha"] = 1
if "zorder" not in self.scatterplot_kws["scatter_kws"].keys():
self.scatterplot_kws["scatter_kws"]["zorder"] = 4
else:
self.scatterplot_kws["scatter_kws"] = {
"s": 3,
"cmap": "winter",
"alpha": 1,
"zorder": 4
}
elif scatterplotEnabled:
raise Exception(
"The input argument 'scatterplot_kws' must be None or a dictionary,\n"
+
"each (key,value) pair of which represents an (attribute,value)\n"
+ "of ParaMonte library's ScatterPlot() class.")
if self.colorbar_kws == (): self.colorbar_kws = {}
#########################
if self._isdryrun: return
#########################
# check rows presence
if self.rows is None:
rowindex = range(len(self._dfref().index))
else:
rowindex = self.rows
# check columns presence
colnames, colindex = dfutils.getColNamesIndex(self._dfref().columns,
self.columns)
# make pairgrid plot
import seaborn as _sns
from matplotlib import pyplot as _plt
self.currentFig = ParaMonteFigure()
if self.set_kws is not None: _sns.set(**self.set_kws)
self.currentFig.pairgrid = _sns.PairGrid(
self._dfref()[colnames].iloc[rowindex, :])
self.currentFig.figure = self.currentFig.pairgrid.fig
# hide axes as requested
if (lsUpperEnabled or kdeUpperEnabled):
self._upperEnabled = True
else:
self.hide("upper")
self._upperEnabled = False
if (lsLowerEnabled or kdeLowerEnabled):
self._lowerEnabled = True
else:
self.hide("lower")
self._lowerEnabled = False
if distplotEnabled:
self._diagEnabled = True
else:
self._diagEnabled = False
self.hide("diag")
# adjust subplot interspaces
self.currentFig.pairgrid.fig.tight_layout()
self.currentFig.pairgrid.fig.subplots_adjust(hspace=0.05, wspace=0.05)
# set up figure layout if needed
# check data type
noDataPassed = ""
if self._dfref is None:
noDataPassed = "It appears that no data has been passed for plotting.\n"
elif not isinstance(self._dfref, _wref.ref):
noDataPassed = "It appears that you have messed with the\ninternal representation of data in the object.\n"
elif not isinstance(self._dfref(), _pd.DataFrame):
noDataPassed = "The input data is not a pandas' dataframe.\n"
if noDataPassed:
raise Exception(
noDataPassed +
"The input data must be a pandas' dataframe.\n" +
"Please pass a dataFrame to the constructor or at\n" +
"the time of calling the object (which is callable with\n" +
"the same input arguments as the object's constructor.")
#########################
# define currentFig components
nrow = len(self.currentFig.pairgrid.axes[:])
nlsplotStr = str(
(lsUpperEnabled + lsLowerEnabled) * nrow * (nrow - 1) // 2)
nkdeplotStr = str(
(kdeUpperEnabled + kdeLowerEnabled) * nrow * (nrow - 1) // 2)
self.currentFig.targetList = [[[] for j in range(nrow)]
for i in range(nrow)]
#self.currentFig.kdeplotList = [ [ [] for j in range(nrow) ] for i in range(nrow) ]
self.currentFig.lineplotList = [[[] for j in range(nrow)]
for i in range(nrow)]
self.currentFig.scatterplotList = [[[] for j in range(nrow)]
for i in range(nrow)]
#self.currentFig.distplotList = [ [] for i in range(nrow) ]
#####################################
#### add distplots as needed
#####################################
if distplotEnabled:
self._timer.tic(
msg="adding the diagonal histograms (distplots)... ", end=_eol)
self.currentFig.pairgrid.map_diag(_sns.distplot,
**self.distplot_kws)
self._timer.toc()
# if distplotEnabled:
#
# msg.note( msg = "adding the diagonal histograms (distplots)...", methodName = self._methodName )
#
# counter = 0
# for irow, row in enumerate(self.currentFig.pairgrid.axes[:]):
#
# counter += 1
# self._timer.tic( msg = " " + str(counter) + " out of " + nlsplotStr + ": " + colnames[irow] + " - " + colnames[irow] + "... ", end = _eol )
#
# ax = row[irow]
# _plt.sca(ax)
#
# currentXlim = ax.get_xlim()
# currentYlim = ax.get_ylim()
#
# self.currentFig.distplotList[irow] = HistPlot ( dataFrame = self._dfref()
# , columns = colnames[irow]
# , rows = self.rows
# , figure_kws = None
# , legend_kws = None
# , set_kws = self.set_kws
# , distplot_kws = self.distplot_kws
# )
# self.currentFig.distplotList[irow].plot()
#
# if self._lowerEnabled:
# ax.set_xlabel("")
# ax.set_ylabel("")
#
# ax.set_xlim(currentXlim)
# ax.set_ylim(currentYlim)
#
# self._timer.toc()
#
# _plt.tight_layout()
#####################################
#### add line/scatter plots as needed
#####################################
if lsplotEnabled:
msg.note(msg="adding the line/scatter plots...",
methodName=self._methodName)
counter = 0
for irow, row in enumerate(self.currentFig.pairgrid.axes[:]):
for icol, ax in enumerate(row):
self.currentFig.targetList[irow][icol] = Target(axes=ax)
if (icol > irow
and lsUpperEnabled) or (icol < irow
and lsLowerEnabled):
counter += 1
self._timer.tic(msg=" " + str(counter) +
" out of " + nlsplotStr + ": " +
colnames[icol] + " - " +
colnames[irow] + "... ",
end=_eol)
_plt.sca(ax)
#_sns.set( self.set_kws )
if lineplotEnabled:
self.currentFig.lineplotList[irow][
icol] = LinePlot(dataFrame=self._dfref(),
xcolumns=colnames[icol],
ycolumns=colnames[irow],
rows=self.rows,
**self.lineplot_kws)
self.currentFig.lineplotList[irow][icol].plot()
if scatterplotEnabled:
self.currentFig.scatterplotList[irow][
icol] = ScatterPlot(dataFrame=self._dfref(),
xcolumns=colnames[icol],
ycolumns=colnames[irow],
rows=self.rows,
**self.scatterplot_kws)
self.currentFig.scatterplotList[irow][icol].plot()
#ax.get_xaxis().set_visible(False)
#ax.get_yaxis().set_visible(False)
#if irow < nrow-1: ax.set_xlabel("")
#if icol > 0: ax.set_ylabel("")
#ax.set_xlim(currentXlim)
#ax.set_ylim(currentYlim)
self._timer.toc()
_plt.tight_layout()
#####################################
#### add kdeplots plots as needed
#####################################
if kdeplotEnabled:
msg.note(
msg=
"adding kdeplots... depending on the number of plots, this may take a long while.",
methodName=self._methodName)
if kdeUpperEnabled:
self._timer.tic(
msg=" adding the upper-triangle kdeplots...", end=_eol)
self.currentFig.pairgrid.map_upper(_sns.kdeplot,
**self.kdeplot_kws)
self._timer.toc()
if kdeLowerEnabled:
self._timer.tic(
msg=" adding the lower-triangle kdeplots...", end=_eol)
self.currentFig.pairgrid.map_lower(_sns.kdeplot,
**self.kdeplot_kws)
self._timer.toc()
if self.outputFile is not None:
self.currentFig.figure.savefig(self.outputFile,
bbox_inches='tight',
pad_inches=0.0)
# set the ticks and labels
nrowMinusOne = nrow - 1
from matplotlib.pyplot import setp
for irow, row in enumerate(self.currentFig.pairgrid.axes[:]):
for icol, ax in enumerate(row):
if self._lowerEnabled:
if icol > 0:
ax.set_ylabel("")
if irow < nrowMinusOne:
ax.set_xlabel("")
elif self._upperEnabled:
if (not kdeplotEnabled):
if icol != irow:
ax.set_ylabel("")
ax.set_xlabel("")
if icol == irow:
ax.set_xlabel(colnames[irow])
ax.set_ylabel(colnames[icol])
ax.xaxis.set_tick_params(which="both",
labelbottom=True)
ax.yaxis.set_tick_params(which="both",
labelbottom=True)
elif icol > irow:
ax.set_ylabel("")
ax.set_xlabel("")
import matplotlib.pyplot as _plt
_plt.subplots_adjust(hspace=0.15, wspace=0.15)
# add colorbar
self._addcbar()
def getFileList(file, fileType, methodName, _mpiDisabled):
suffix = "_" + fileType + ".txt"
if _os.path.isfile(
file): # check if the input path is a full path to a file
FileList = [file]
pattern = file
if suffix != file[-len(suffix):]:
_msg.warn(msg="The name of the input file: \n\n" + " " + file +
"\n\n" + "does not end with the expected suffix '" +
suffix + "' for a " + fileType + " file type.\n",
methodName=methodName,
marginTop=1,
marginBot=1)
elif _os.path.isdir(file): # ensure the input path is not a directory
_msg.abort(
msg="file='" + file + "' cannot point to a directory.\n" +
"Provide a string as the value of file that points to a unique " +
fileType + " file or\n" +
"to the unique name (including path) of the simulation name shared among its output files.\n",
methodName=methodName,
marginTop=1,
marginBot=1)
else:
# search for files matching the input pattern
import glob
if file[-1:] == "*":
pattern = file
else:
pattern = file + "*" # + suffix
_ = glob.glob(pattern)
FileList = []
for filename in _:
if suffix in filename: FileList.append(filename)
if len(FileList) == 0:
_msg.abort(
msg="Failed to detect any " + fileType +
" files with the requested pattern: \n\n" + " " + pattern +
"\n\n" +
"Provide a string, as the value of the input argument 'file', that either \n\n"
+ " - points to one or more " + fileType +
" files, or, \n" +
" - represents the unique name of a ParaMonte simulation. \n"
+
" This unique-name is the common prefix in the names of \n"
+ " the output files of a ParaMonte simulation.",
methodName=methodName,
marginTop=1,
marginBot=1)
else:
pattern += suffix
if _mpiDisabled:
_msg.note(msg=str(len(FileList)) +
' files detected matching the pattern: "' + pattern + '"',
methodName=methodName,
marginTop=0,
marginBot=0)
return FileList
def getFileList(file, fileSuffix, methodName, reportEnabled = True):
FileList = []
iswebfile = False
fullSuffix = "_" + fileSuffix + ".txt"
if os.path.isfile(file):
# check if the input path is a full path to a file
FileList.append(file)
pattern = file
if fullSuffix != file[-len(fullSuffix):]:
err.warn( msg = "The name of the input file: \n\n"
+ " " + file + "\n\n"
+ "does not end with the expected suffix '" + fullSuffix + "' for a " + fileSuffix + " file type.\n"
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
else:
import glob
pattern = "" # not really needed, but just in case...
for i in [1,2]:
if i==1:
#### first search for files matching the input pattern, then for directory
pattern = file if "*" in file else file + "*" # + fullSuffix
elif i==2:
#### then search for file as directory
if os.path.isdir(file):
pattern = os.path.join(file, "*" + fullSuffix)
if reportEnabled:
err.warn( msg = "file='" + file + "' points to a directory.\n"
+ "Now searching inside the folder for a " + fileSuffix + " file..."
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
#### now search for pattern
for filePath in glob.glob(pattern):
if filePath.endswith(fullSuffix):
FileList.append(filePath)
if len(FileList)>0: break
if not pattern.endswith(fullSuffix): pattern += fullSuffix
if len(FileList)==0:
#### one last try, search the web
try:
import urllib.request
#filePath = getRandomFilePrefix(prefix = methodName + "_" + fileSuffix)
localFilePath, headers = urllib.request.urlretrieve(url = file)
FileList.append(localFilePath)
iswebfile = True
except:
err.abort ( msg = "Failed to detect any " + fileSuffix + " files with the requested pattern: \n\n"
+ " " + pattern + "\n\n"
+ "Provide a string, as the value of the input argument ``file``, that either \n\n"
+ " - points to one or more " + fileSuffix + " files, or, \n"
+ " - represents the unique name of a ParaMonte simulation. \n"
+ " This unique-name is the common prefix in the names of \n"
+ " the output files of a ParaMonte simulation.\n\n"
+ "Most importantly, ensure the requested file is in ASCII format.\n"
+ "The binary-format chain or restart output files cannot be parsed.\n"
+ "You can request ASCII-format output files by setting the\n"
+ "appropriate simulation specifications of the " + methodName + " sampler,\n\n"
+ " spec.restartFileFormat = \"ascii\"\n"
+ " spec.chainFileFormat = \"ascii\""
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
elif reportEnabled:
err.note( msg = str(len(FileList)) + ' files detected matching the pattern: "' + pattern + '"'
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
return FileList, iswebfile
def getFileList(file, fileSuffix, methodName, reportEnabled):
fullSuffix = "_" + fileSuffix + ".txt"
if os.path.isfile(file):
# check if the input path is a full path to a file
FileList = [file]
pattern = file
if fullSuffix != file[-len(fullSuffix):]:
err.warn( msg = "The name of the input file: \n\n"
+ " " + file + "\n\n"
+ "does not end with the expected suffix '" + fullSuffix + "' for a " + fileSuffix + " file type.\n"
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
else:
if os.path.isdir(file):
# ensure the input path is not a directory
err.warn( msg = "file='" + file + "' points to a directory.\n"
+ "Now searching inside the folder for a " + fileSuffix + " file..."
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
pattern = os.path.join(file, "*" + fullSuffix)
else:
# search for files matching the input pattern
if "*" in file: # file[-1:]=="*":
pattern = file
else:
pattern = file + "*" # + fullSuffix
import glob
_ = glob.glob(pattern)
FileList = []
for filePath in _:
if filePath.endswith(fullSuffix):
FileList.append(filePath)
if not pattern.endswith(fullSuffix): pattern += fullSuffix
if len(FileList)==0:
err.abort ( msg = "Failed to detect any " + fileSuffix + " files with the requested pattern: \n\n"
+ " " + pattern + "\n\n"
+ "Provide a string, as the value of the input argument ``file``, that either \n\n"
+ " - points to one or more " + fileSuffix + " files, or, \n"
+ " - represents the unique name of a ParaMonte simulation. \n"
+ " This unique-name is the common prefix in the names of \n"
+ " the output files of a ParaMonte simulation.\n\n"
+ "Most importantly, ensure the requested file is in ASCII format.\n"
+ "The binary-format chain or restart output files cannot be parsed.\n"
+ "You can request ASCII-format output files by setting the\n"
+ "appropriate simulation specifications of the " + methodName + " sampler,\n\n"
+ " spec.restartFileFormat = \"ascii\"\n"
+ " spec.chainFileFormat = \"ascii\""
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
elif reportEnabled:
err.note( msg = str(len(FileList)) + ' files detected matching the pattern: "' + pattern + '"'
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
return FileList