Ref/remote download

SimPEG/EM/Base.py

@@ -256,7 +256,9 @@ def MeSigmaI(self):
         Inverse of the edge inner product matrix for \\(\\sigma\\).
         """
         if getattr(self, '_MeSigmaI', None) is None:
-            self._MeSigmaI = self.mesh.getEdgeInnerProduct(self.sigma, invMat=True)
+            self._MeSigmaI = self.mesh.getEdgeInnerProduct(
+                self.sigma, invMat=True
+            )
         return self._MeSigmaI
 
     # TODO: This should take a vector
@@ -425,7 +427,7 @@ def s_e(self, prob):
         """
         return Utils.Zero()
 
-    def s_mDeriv(self, prob, v, adjoint = False):
+    def s_mDeriv(self, prob, v, adjoint=False):
         """
         Derivative of magnetic source term with respect to the inversion model
 
@@ -438,7 +440,7 @@ def s_mDeriv(self, prob, v, adjoint = False):
 
         return Utils.Zero()
 
-    def s_eDeriv(self, prob, v, adjoint = False):
+    def s_eDeriv(self, prob, v, adjoint=False):
         """
         Derivative of electric source term with respect to the inversion model
 

SimPEG/Utils/__init__.py

@@ -23,3 +23,4 @@
 from .coordutils import rotatePointsFromNormals, rotationMatrixFromNormals
 from .modelutils import surface2ind_topo
 from .PlotUtils import plot2Ddata, plotLayer
+from .io_utils import download

SimPEG/Utils/io_utils.py

@@ -1,8 +1,8 @@
 from __future__ import print_function
 import numpy as np
-from SimPEG import Mesh
 import time as tm
 import re
+import warnings
 
 
 def read_GOCAD_ts(tsfile):
@@ -146,35 +146,90 @@ def surface2inds(vrtx, trgl, mesh, boundaries=True, internal=True):
     return insideGrid
 
 
-def remoteDownload(url, remoteFiles, basePath=None):
+def download(
+    url, path='.', overwrite=False, verbose=True
+):
     """
     Function to download all files stored in a cloud directory
-    var:    url ("http:\\...")
-    list:   List of file names to download
+
+    :param str url: url or list of urls for the file(s) to be downloaded ("https://...")
+    :param str path: path to where the directory is created and files downloaded (default is the current directory)
+    :param bool overwrite: overwrite if a file with the specified name already exists
+    :param bool verbose: print out progress
     """
 
     # Download from cloud
     import urllib
-    import shutil
     import os
     import sys
+
+    def rename_path(downloadpath):
+        splitfullpath = downloadpath.split(os.path.sep)
+
+        # grab just the filename
+        fname = splitfullpath[-1]
+        fnamesplit = fname.split('.')
+        newname = fnamesplit[0]
+
+        # check if we have already re-numbered
+        newnamesplit = newname.split('(')
+
+        # add (num) to the end of the filename
+        if len(newnamesplit) == 1:
+            num = 1
+        else:
+            num = int(newnamesplit[-1][:-1])
+            num += 1
+
+        newname = '{}({}).{}'.format(newnamesplit[0], num, fnamesplit[-1])
+        return os.path.sep.join(
+            splitfullpath[:-1] + newnamesplit[:-1] + [newname]
+        )
+
+    # grab the correct url retriever
     if sys.version_info < (3,):
         urlretrieve = urllib.urlretrieve
     else:
         urlretrieve = urllib.request.urlretrieve
 
-    if basePath is None:
-        basePath = os.curdir+os.path.sep+'SimPEGtemp'+os.path.sep
-
-    if os.path.exists(basePath):
-        shutil.rmtree(basePath)
-
-    os.makedirs(basePath)
-
-    print("Download files from URL...")
-    for file in remoteFiles:
-        print("Retrieving: " + file)
-        urlretrieve(url + file, basePath+file)
+    # ensure we are working with absolute paths and home directories dealt with
+    path = os.path.abspath(os.path.expanduser(path))
+
+    # make the directory if it doesn't currently exist
+    if not os.path.exists(path):
+        os.makedirs(path)
+
+    if isinstance(url, str):
+        filenames = [url.split('/')[-1]]
+    elif isinstance(url, list):
+        filenames = [u.split('/')[-1] for u in url]
+
+    downloadpath = [os.path.sep.join([path, f]) for f in filenames]
+
+    # check if the directory already exists
+    for i, download in enumerate(downloadpath):
+        if os.path.exists(download):
+            if overwrite is True:
+                if verbose is True:
+                    print("overwriting {}".format(download))
+            elif overwrite is False:
+                while os.path.exists is True:
+                    download = rename_path(download)
+
+                if verbose is True:
+                    print(
+                        "file already exists, new file is called {}".format(
+                            download
+                        )
+                    )
+                downloadpath[i] = download
+
+    # download files
+    urllist = url if isinstance(url, list) else [url]
+    for u, f in zip(urllist, downloadpath):
+        print("Downloading {}...".format(u))
+        urlretrieve(u, f)
+        print("   saved to: " + f)
 
     print("Download completed!")
-    return basePath
+    return downloadpath if isinstance(url, list) else downloadpath[0]

examples/04-grav/plot_laguna_del_maule_inversion.py

@@ -16,7 +16,7 @@
 import SimPEG.PF as PF
 from SimPEG import Maps, Regularization, Optimization, DataMisfit,\
                    InvProblem, Directives, Inversion
-from SimPEG.Utils.io_utils import remoteDownload
+from SimPEG.Utils.io_utils import download
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -25,14 +25,18 @@ def run(plotIt=True, cleanAfterRun=True):
 
     # Start by downloading files from the remote repository
     url = "https://storage.googleapis.com/simpeg/Chile_GRAV_4_Miller/"
-    cloudfiles = ['LdM_grav_obs.grv', 'LdM_mesh.mesh',
-                  'LdM_topo.topo', 'LdM_input_file.inp']
-
-    basePath = os.path.sep.join(os.path.abspath(os.getenv('HOME')).split
-                                (os.path.sep)+['Downloads']+['SimPEGtemp'])
-    basePath = os.path.abspath(remoteDownload(url,
-                                              cloudfiles,
-                                              basePath=basePath+os.path.sep))
+    cloudfiles = [
+        'LdM_grav_obs.grv', 'LdM_mesh.mesh',
+        'LdM_topo.topo', 'LdM_input_file.inp'
+    ]
+
+    # Download to Downloads/SimPEGtemp
+    basePath = download(
+        [url+f for f in cloudfiles],
+        path='~/Downloads/simpegtemp',
+        overwrite=True
+    )
+
     input_file = basePath + os.path.sep + 'LdM_input_file.inp'
     # %% User input
     # Plotting parameters, max and min densities in g/cc

examples/07-fdem/plot_heagyetal2016_casing.py

@@ -7,7 +7,7 @@
 from SimPEG import Mesh, Utils, Maps, Tests
 from SimPEG.EM import mu_0, FDEM, Analytics
 from SimPEG.EM.Utils import omega
-from SimPEG.Utils.io_utils import remoteDownload
+from SimPEG.Utils.io_utils import download
 # try:
 #     from pymatsolver import MumpsSolver as Solver
 #     print('using MumpsSolver')
@@ -1243,42 +1243,25 @@ class PrimSecCasingStoredResults(PrimSecCasingExample):
         'J_PrimSec_5e6Casing_50Mu_05Hz_LargeCondBody',
     ]
 
-    @property
-    def filepath(self):
-        return os.path.sep.join(
-            os.path.abspath(os.getenv('HOME')).split(os.path.sep) +
-            ['Downloads'] + ['SimPEGtemp']
-        )
-
-    def downloadStoredResults(self):
-        # download the results from where they are stored on google app engine
-
-        return os.path.abspath(
-            remoteDownload(
-                self.url, [self.cloudfile], basePath=self.filepath+os.path.sep
-            )
-        )
-
     def removeStoredResults(self):
         import shutil
         print('Removing {}'.format(self.filepath))
         shutil.rmtree(self.filepath)
 
     def run(self, plotIt=False, runTests=False, saveFig=False):
 
-        self.downloadStoredResults()
+        filepath = download(
+            self.url + self.cloudfile, path='~/Downloads/simpegtemp',
+            overwrite=True
+        )
+        self.filepath = os.path.sep.join(filepath.split(os.path.sep)[:-1])
 
         # resultsFiles = ['{filepath}{slash}{file}'.format(
         #     filepath=self.filepath, slash=os.path.sep, file=file)
         #     for file in self.cloudfiles]
         # results = [np.load(file, encoding='bytes') for file in resultsFiles]
 
-        h5f = h5py.File(
-            '{filepath}{slash}{file}'.format(
-                filepath=self.filepath, slash=os.path.sep, file=self.cloudfile
-                ), 'r'
-            )
-
+        h5f = h5py.File(filepath, 'r')
         results = [h5f[entry_name][:] for entry_name in self.entry_names]
         results = dict(zip(['primfields', 'dpredback', 'dpred', 'J'], results))
 

tests/base/test_utils.py

@@ -2,14 +2,18 @@
 import unittest
 import numpy as np
 import scipy.sparse as sp
+import os
+import shutil
 from SimPEG.Utils import (
     sdiag, sub2ind, ndgrid, mkvc, inv2X2BlockDiagonal,
     inv3X3BlockDiagonal, invPropertyTensor, makePropertyTensor, indexCube,
-    ind2sub, asArray_N_x_Dim, TensorType, diagEst, count, timeIt, Counter
+    ind2sub, asArray_N_x_Dim, TensorType, diagEst, count, timeIt, Counter,
+    download
 )
 from SimPEG import Mesh
 from SimPEG.Tests import checkDerivative
 
+
 TOL = 1e-8
 
 
@@ -303,5 +307,30 @@ def testProbing(self):
         self.assertTrue(err < TOL)
 
 
+class TestDownload(unittest.TestCase):
+    def test_downloads(self):
+        url = "https://storage.googleapis.com/simpeg/Chile_GRAV_4_Miller/"
+        cloudfiles = [
+            'LdM_grav_obs.grv', 'LdM_mesh.mesh',
+            'LdM_topo.topo', 'LdM_input_file.inp'
+        ]
+
+        url1 = url + cloudfiles[0]
+        url2 = url + cloudfiles[1]
+
+        file_names = download(
+            [url1, url2], path='./test_urls', overwrite=True
+        )
+        # or
+        file_name = download(url1, path='./test_url', overwrite=True)
+        # where
+        assert isinstance(file_names, list)
+        assert len(file_names) == 2
+        assert isinstance(file_name, str)
+
+        # clean up
+        shutil.rmtree(os.path.expanduser('./test_urls'))
+        shutil.rmtree(os.path.expanduser('./test_url'))
+
 if __name__ == '__main__':
     unittest.main()

tests/pf/test_gravity_IO.py

@@ -4,6 +4,7 @@
 from SimPEG.Utils import io_utils
 from scipy.constants import mu_0
 import shutil
+import os
 
 
 class MagSensProblemTests(unittest.TestCase):
@@ -13,11 +14,16 @@ def setUp(self):
         cloudfiles = ['GravData.obs', 'Gaussian.topo', 'Mesh_10m.msh',
                       'ModelStart.sus', 'SimPEG_Grav_Input.inp']
 
-        self.basePath = io_utils.remoteDownload(url, cloudfiles)
+        self.basePath = os.path.expanduser('~/Downloads/simpegtemp')
+        self.files = io_utils.download(
+            [url + f for f in cloudfiles],
+            path=self.basePath,
+            overwrite=True
+        )
 
     def test_magnetics_inversion(self):
 
-        inp_file = self.basePath + 'SimPEG_Grav_Input.inp'
+        inp_file = os.path.sep.join([self.basePath, 'SimPEG_Grav_Input.inp'])
 
         driver = PF.GravityDriver.GravityDriver_Inv(inp_file)
 
@@ -36,8 +42,12 @@ def test_magnetics_inversion(self):
         print(driver.eps)
 
         # Write obs to file
-        PF.Gravity.writeUBCobs(self.basePath + 'FWR_data.dat',
-                               driver.survey, driver.survey.dobs)
+        PF.Gravity.writeUBCobs(
+            os.path.sep.join(
+                [self.basePath, 'FWR_data.dat']
+            ),
+            driver.survey, driver.survey.dobs
+        )
 
         # Clean up the working directory
         shutil.rmtree(self.basePath)

tests/pf/test_magnetics_IO.py

@@ -4,6 +4,7 @@
 from SimPEG.Utils import io_utils
 from scipy.constants import mu_0
 import shutil
+import os
 
 
 class MagSensProblemTests(unittest.TestCase):
@@ -13,11 +14,14 @@ def setUp(self):
         cloudfiles = ['MagData.obs', 'Gaussian.topo', 'Mesh_10m.msh',
                       'ModelStart.sus', 'SimPEG_Mag_Input.inp']
 
-        self.basePath = io_utils.remoteDownload(url, cloudfiles)
+        self.basePath = os.path.expanduser('~/Downloads/simpegtemp')
+        self.files = io_utils.download(
+            [url+f for f in cloudfiles], path=self.basePath, overwrite=True
+        )
 
     def test_magnetics_inversion(self):
 
-        inp_file = self.basePath + 'SimPEG_Mag_Input.inp'
+        inp_file = os.path.sep.join([self.basePath, 'SimPEG_Mag_Input.inp'])
 
         driver = PF.MagneticsDriver.MagneticsDriver_Inv(inp_file)
 
@@ -36,8 +40,10 @@ def test_magnetics_inversion(self):
         print(driver.eps)
 
         # Write obs to file
-        PF.Magnetics.writeUBCobs(self.basePath + 'FWR_data.dat',
-                                 driver.survey, driver.survey.dobs)
+        PF.Magnetics.writeUBCobs(
+            os.path.sep.join([self.basePath, 'FWR_data.dat']),
+            driver.survey, driver.survey.dobs
+        )
 
         # Clean up the working directory
         shutil.rmtree(self.basePath)