flopy 3.2.1__zip → 3.2.2__zip

flopy-3.2.2/flopy/utils/modpathfile.py

@@ -0,0 +1,421 @@
+"""
+Module to read MODPATH output files.  The module contains three
+important classes that can be accessed by the user.
+
+*  PathlineFile (Binary head file.  Can also be used for drawdown)
+
+"""
+
+import numpy as np
+from collections import OrderedDict
+
+class PathlineFile():
+    """
+    PathlineFile Class.
+
+    Parameters
+    ----------
+    filename : string
+        Name of the concentration file
+    verbose : bool
+        Write information to the screen.  Default is False.
+
+    Attributes
+    ----------
+
+    Methods
+    -------
+
+    See Also
+    --------
+
+    Notes
+    -----
+    The PathlineFile class provides simple ways to retrieve MODPATH 6
+    pathline data from a MODPATH 6 ascii pathline file.
+
+    Examples
+    --------
+
+    >>> import flopy
+    >>> pthobj = flopy.utils.PathlineFile('model.mppth')
+    >>> p1 = pthobj.get_data(partid=1)
+
+
+    """
+    def __init__(self, filename, verbose=False):
+        self.fname = filename
+        self.dtype, self.outdtype = self._get_dtypes()
+        self._build_index()
+        self._data = np.loadtxt(self.file, dtype=self.dtype, skiprows=self.skiprows)
+        # set number of particle ids
+        self.nid = self._data['particleid'].max()
+        # convert layer, row, and column indices; particle id and group; and
+        #  line segment indices to zero-based
+        self._data['k'] -= 1
+        self._data['i'] -= 1
+        self._data['j'] -= 1
+        self._data['particleid'] -= 1
+        self._data['particlegroup'] -= 1
+        self._data['linesegmentindex'] -= 1
+        # close the input file
+        self.file.close()
+        return
+        
+    def _build_index(self):
+        """
+           Set position of the start of the pathline data.
+        """
+        self.skiprows = 0
+        self.file = open(self.fname, 'r')
+        while True:
+            line = self.file.readline()
+            self.skiprows += 1
+            if 'end header' in line.lower():
+                break
+        self.file.seek(0)
+
+    def _get_dtypes(self):
+        """
+           Build numpy dtype for the MODPATH 6 pathline file.
+        """
+        dtype = np.dtype([("particleid", np.int), ("particlegroup", np.int),
+                          ("timepointindex", np.int), ("comulativetimestep", np.int),
+                          ("time", np.float32), ("x", np.float32),
+                          ("y", np.float32), ("z", np.float32),
+                          ("k", np.int), ("i", np.int), ("j", np.int),
+                          ("grid", np.int), ("xloc", np.float32), 
+                          ("yloc", np.float32), ("zloc", np.float32),
+                          ("linesegmentindex", np.int)])
+        outdtype = np.dtype([("x", np.float32), ("y", np.float32), ("z", np.float32),
+                             ("time", np.float32), ("k", np.int), ("id", np.int)])
+        return dtype, outdtype
+                              
+
+    def get_maxid(self):
+        """
+        Get the maximum pathline number in the file pathline file
+
+        Returns
+        ----------
+        out : int
+            Maximum pathline number.
+
+        """
+        return self.maxid
+
+
+    def get_maxtime(self):
+        """
+        Get the maximum time in pathline file
+
+        Returns
+        ----------
+        out : float
+            Maximum pathline timer.
+
+        """
+        return self.data['time'].max()
+
+
+    def get_data(self, partid=0, totim=None, ge=True):
+        """
+        get pathline data from the pathline file for a single pathline.
+
+        Parameters
+        ----------
+        partid : int
+            The zero-based particle id.  The first record is record 0.
+        totim : float
+            The simulation time. All pathline points for particle partid
+            that are greater than or equal to (ge=True) or less than or
+            equal to (ge=False) totim will be returned. Default is None
+        ge : bool
+            Boolean that determines if pathline times greater than or equal
+            to or less than or equal to totim is used to create a subset
+            of pathlines. Default is True.
+
+        Returns
+        ----------
+        ra : numpy record array
+            A numpy recarray with the x, y, z, time, k, and particleid for
+            pathline partid.
+
+
+        See Also
+        --------
+
+        Notes
+        -----
+
+        Examples
+        --------
+
+        >>> import flopy.utils.modpathfile as mpf
+        >>> pthobj = flopy.utils.PathlineFile('model.mppth')
+        >>> p1 = pthobj.get_data(partid=1)
+
+        """
+        idx = self._data['particleid'] == partid
+        if totim is not None:
+            if ge:
+                idx = (self._data['time'] >= totim) & (self._data['particleid'] == partid)
+            else:
+                idx = (self._data['time'] <= totim) & (self._data['particleid'] == partid)
+        else:
+            idx = self._data['particleid'] == partid
+        self._ta = self._data[idx]
+        ra = np.rec.fromarrays((self._ta['x'], self._ta['y'], self._ta['z'],
+                                self._ta['time'], self._ta['k'], self._ta['particleid']), dtype=self.outdtype)
+        return ra
+
+    def get_alldata(self, totim=None, ge=True):
+        """
+        get pathline data from the pathline file for all pathlines and all times.
+
+        Parameters
+        ----------
+        totim : float
+            The simulation time. All pathline points for particle partid
+            that are greater than or equal to (ge=True) or less than or
+            equal to (ge=False) totim will be returned. Default is None
+        ge : bool
+            Boolean that determines if pathline times greater than or equal
+            to or less than or equal to totim is used to create a subset
+            of pathlines. Default is True.
+
+        Returns
+        ----------
+        plist : a list of numpy record array
+            A list of numpy recarrays with the x, y, z, time, k, and particleid for
+            all pathlines.
+
+
+        See Also
+        --------
+
+        Notes
+        -----
+
+        Examples
+        --------
+
+        >>> import flopy.utils.modpathfile as mpf
+        >>> pthobj = flopy.utils.PathlineFile('model.mppth')
+        >>> p = pthobj.get_alldata()
+
+        """
+        plist = []
+        for partid in range(self.nid):
+            plist.append(self.get_data(partid=partid, totim=totim, ge=ge))
+        return plist
+
+
+class EndpointFile():
+    """
+    EndpointFile Class.
+
+    Parameters
+    ----------
+    filename : string
+        Name of the concentration file
+    verbose : bool
+        Write information to the screen.  Default is False.
+
+    Attributes
+    ----------
+
+    Methods
+    -------
+
+    See Also
+    --------
+
+    Notes
+    -----
+    The EndpointeFile class provides simple ways to retrieve MODPATH 6
+    endpoint data from a MODPATH 6 ascii endpoint file.
+
+    Examples
+    --------
+
+    >>> import flopy
+    >>> endobj = flopy.utils.EndpointFile('model.mpend')
+    >>> e1 = endobj.get_data(partid=1)
+
+
+    """
+    def __init__(self, filename, verbose=False):
+        self.fname = filename
+        self.dtype, self.outdtype = self._get_dtypes()
+        self._build_index()
+        self._data = np.loadtxt(self.file, dtype=self.dtype, skiprows=self.skiprows)
+        # set number of particle ids
+        self.nid = self._data['particleid'].max()
+        # convert layer, row, and column indices; particle id and group; and
+        #  line segment indices to zero-based
+        self._data['k0'] -= 1
+        self._data['i0'] -= 1
+        self._data['j0'] -= 1
+        self._data['k'] -= 1
+        self._data['i'] -= 1
+        self._data['j'] -= 1
+        self._data['particleid'] -= 1
+        self._data['particlegroup'] -= 1
+        # close the input file
+        self.file.close()
+        return
+
+    def _build_index(self):
+        """
+           Set position of the start of the pathline data.
+        """
+        self.skiprows = 0
+        self.file = open(self.fname, 'r')
+        idx = 0
+        while True:
+            line = self.file.readline()
+            self.skiprows += 1
+            if idx == 1:
+                t = line.strip()
+                self.direction = 1
+                if int(t[0]) == 2:
+                    self.direction = -1
+            if 'end header' in line.lower():
+                break
+        self.file.seek(0)
+
+    def _get_dtypes(self):
+        """
+           Build numpy dtype for the MODPATH 6 endpoint file.
+        """
+        dtype = np.dtype([("particleid", np.int), ("particlegroup", np.int),
+                          ('status', np.int), ('initialtime', np.float32),
+                          ('finaltime', np.float32), ('initialgrid', np.int),
+                          ('k0', np.int), ('i0', np.int),
+                          ('j0', np.int), ('initialcellface', np.int),
+                          ('initialzone', np.int), ('xloc0', np.float32),
+                          ('yloc0', np.float32), ('zloc0', np.float32),
+                          ('x0', np.float32), ('y0', np.float32), ('z0', np.float32),
+                          ('finalgrid', np.int), ('k', np.int), ('i', np.int),
+                          ('j', np.int), ('finalcellface', np.int),
+                          ('finalzone', np.int), ('xloc', np.float32),
+                          ('yloc', np.float32), ('zloc', np.float32),
+                          ('x', np.float32), ('y', np.float32), ('z', np.float32),
+                          ('label', '|S40')])
+        outdtype = np.dtype([("x", np.float32), ("y", np.float32), ("z", np.float32),
+                             ("time", np.float32), ("k", np.int), ("id", np.int)])
+        return dtype, outdtype
+
+
+    def get_maxid(self):
+        """
+        Get the maximum endpoint particle id in the file endpoint file
+
+        Returns
+        ----------
+        out : int
+            Maximum enpoint particle id.
+
+        """
+        return self.maxid
+
+
+    def get_maxtime(self):
+        """
+        Get the maximum time in endpoint file
+
+        Returns
+        ----------
+        out : float
+            Maximum endpoint time.
+
+        """
+        return self.data['finaltime'].max()
+
+
+    def get_data(self, partid=0, final=True):
+        """
+        get endpoint data from the endpoint file for a single particle.
+
+        Parameters
+        ----------
+        partid : int
+            The zero-based particle id.  The first record is record 0.
+        final : bool
+            Boolean flag used determine if the initial or final endpoint
+            time should be returned, Default is True
+
+        Returns
+        ----------
+        ra : numpy record array
+            A numpy recarray with the final or initial (final=False)
+            x, y, z, time, k, and particleid for endpoint partid.
+
+
+        See Also
+        --------
+
+        Notes
+        -----
+
+        Examples
+        --------
+
+        >>> import flopy
+        >>> endobj = flopy.utils.EndpointFile('model.mpend')
+        >>> e1 = endobj.get_data(partid=1)
+
+        """
+        idx = self._data['particleid'] == partid
+        self._ta = self._data[idx]
+        if final:
+            ra = np.rec.fromarrays((self._ta['x'], self._ta['y'], self._ta['z'],
+                                    self._ta['finaltime'], self._ta['k'],
+                                    self._ta['particleid']), dtype=self.outdtype)
+        else:
+            ra = np.rec.fromarrays((self._ta['x0'], self._ta['y0'], self._ta['z0'],
+                                    self._ta['initialtime'], self._ta['k0'],
+                                    self._ta['particleid']), dtype=self.outdtype)
+        return ra
+
+    def get_alldata(self, final=True):
+        """
+        get endpoint data from the endpoint file for all endpoints.
+
+        Parameters
+        ----------
+        final : bool
+            Boolean flag used determine if the initial or final endpoint
+            time should be returned, Default is True
+
+        Returns
+        ----------
+        ra : numpy record array
+            A numpy recarray with the final or initial (final=False)
+            x, y, z, time, k, and particleid for endpoint partid.
+
+
+        See Also
+        --------
+
+        Notes
+        -----
+
+        Examples
+        --------
+
+        >>> import flopy
+        >>> endobj = flopy.utils.EndpointFile('model.mpend')
+        >>> e = endobj.get_alldata()
+
+        """
+        if final:
+            ra = np.rec.fromarrays((self._data['x'], self._data['y'], self._data['z'],
+                                    self._data['finaltime'], self._data['k'],
+                                    self._data['particleid']), dtype=self.outdtype)
+        else:
+            ra = np.rec.fromarrays((self._data['x0'], self._data['y0'], self._data['z0'],
+                                    self._data['initialtime'], self._data['k0'],
+                                    self._data['particleid']), dtype=self.outdtype)
+        return ra