def delFile(file, desc="the requested file", methodName=""):
try:
import os
os.remove(file)
except:
err.warn( msg = newline
+ "Failed to delete " + desc + " from the local disk. File may be protected. You can try manually deleting it: " + newline
+ newline
+ " " + file + newline
+ newline
, methodName = methodName
, marginTop = 1
, marginBot = 1
)
return None
except:
pass
cmd = None
if platform.isWin32: cmd = "systeminfo > " + platform.systemInfoFilePath
if platform.isLinux:
cmd = "uname -a >> " + platform.systemInfoFilePath + "; lscpu >> " + platform.systemInfoFilePath
if platform.isMacOS:
cmd = "uname -a >> " + platform.systemInfoFilePath + "; sysctl -a | grep machdep.cpu >> " + platform.systemInfoFilePath
if cmd is not None:
err = os.system(cmd)
if err != 0:
platform.systemInfoFilePath = None
warn(msg="Failed to get the system information. skipping...",
methodName=names.paramonte,
marginTop=1,
marginBot=1)
####################################################################################################################################
website = Struct()
website.home = Struct()
website.home.url = "https://www.cdslab.org/paramonte"
website.home.install = Struct()
website.home.install._url = website.home.url + "/notes/installation"
# installation Linux
website.home.overview = Struct()
website.home.overview._url = website.home.url + "/notes/overview"
def get(self, reself: tp.Optional[bool] = False, **kwargs):
"""
Compute the autocorrelations of the selected columns
of the input dataframe to the object's constructor.
**Parameters**
reself
A logical variable. When ``True``, an instance of
the object will be returned to the calling routine
upon exit. The default value is ``False``.
**Returns**
The object if ``reself = True`` otherwise, ``None``.
**NOTE**
This method causes side-effects by manipulating
the existing attributes of the object.
"""
for key in kwargs.keys():
if hasattr(self, key):
setattr(self, key, kwargs[key])
elif key == "dataFrame":
setattr(self, "_dfref", wref.ref(kwargs[key]))
else:
raise Exception("Unrecognized input '" + key +
"' class attribute detected." + newline +
self._getDocString())
############################################################################################################################
#### check columns presence
############################################################################################################################
colnames, colindex = dfutils.getColNamesIndex(self._dfref().columns,
self.columns)
############################################################################################################################
#### check rows presence. This must be checked here, because it depends on the integrity of the in input dataFrame.
############################################################################################################################
if self.rows is None: self.rows = range(len(self._dfref().index))
#rownames = self._dfref().index[self.rows]
############################################################################################################################
#### compute the autocorrelations
############################################################################################################################
self._nvar = len(colnames)
self._nlag = len(self.rows)
acf = np.zeros((self._nvar, self._nlag))
try:
from scipy.signal import correlate
for cnt, ivar in enumerate(colindex):
xdata = self._dfref().iloc[
self.rows, ivar].values.flatten() - np.mean(
self._dfref().iloc[self.rows, ivar].values.flatten())
acf[cnt] = correlate(
xdata, xdata, mode="full")[self._nlag - 1:2 * self._nlag]
acf[cnt] = acf[cnt] / acf[cnt, 0]
except:
if self._reportEnabled:
err.warn(
msg=
"Failed to compute the Autocorrelation function of the input dataFrame."
+ newline +
"This could likely be due to an error in importing the scipy Python library."
+ newline +
"Please make sure you have the scipy library properly installed on your system."
+ newline +
"You can do so by typing the following command on your Anaconda3 or Bash command prompt:"
+ newline + newline +
" pip install --user --upgrade scipy",
methodName=self._methodName,
marginTop=1,
marginBot=1)
self.df = pd.DataFrame(np.transpose(acf))
############################################################################################################################
#### specify columns/index names
############################################################################################################################
colnames = ["ACF_" + colnames[i] for i in range(len(colnames))]
self.df.columns = colnames
############################################################################################################################
#### add SampleLogFunc to df for plot coloring, if exists
############################################################################################################################
ccolumns = ()
if "SampleLogFunc" in self._dfref().columns:
ccolumns = "SampleLogFunc"
self.df.insert(loc=0,
column=ccolumns,
value=self._dfref()[[ccolumns]].values.flatten(),
allow_duplicates=True)
############################################################################################################################
#### add lags to df
############################################################################################################################
self.df.insert(loc=0, column="Lag", value=[i for i in self.df.index])
############################################################################################################################
#### graphics
############################################################################################################################
self._plotTypeList = ["line", "scatter", "lineScatter"]
self._progress.note(msg="adding the autocrrelation graphics tools... ",
end=newline,
pre=True)
self.plot = Struct()
self._resetPlot(resetType="hard")
self.plot.reset = self._resetPlot
############################################################################################################################
if reself: return self
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
