fixes to check.py, mfsfr2.py, modpathfile.py (#294)
* t010 passes * t031 runs * proposed fix to np.core.records.fromarrays issue * t009 passes except for issue with gage package file paths * fixed several np.core.records.fromarrays issues; stuck on t041 a bytes-like object is required, not 'float'develop
aleaf
langevin-usgs
parent
97de43bb19
commit
921b40c009
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@ -6,6 +6,8 @@ import os
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import glob
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import shutil
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import numpy as np
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from flopy.utils.recarray_utils import create_empty_recarray
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try:
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import matplotlib
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# if os.getenv('TRAVIS'): # are we running https://travis-ci.org/ automated tests ?
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@ -47,15 +49,12 @@ sfr_items = {0: {'mfnam': 'test1ss.nam',
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}
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def create_sfr_data():
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r = np.zeros((27, 2), dtype=[('iseg', int), ('ireach', int)])
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r = np.core.records.fromarrays(r.transpose(),
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dtype=[('iseg', int), ('ireach', int)])
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r = create_empty_recarray(27, dtype = [('iseg', int), ('ireach', int)])
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r['iseg'] = sorted(list(range(1, 10)) * 3)
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r['ireach'] = [1, 2, 3] * 9
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d = np.zeros((9, 2), dtype=[('nseg', int), ('outseg', int)])
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d = np.core.records.fromarrays(d.transpose(),
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dtype=[('nseg', int), ('outseg', int)])
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d = create_empty_recarray(9, dtype=[('nseg', int), ('outseg', int)])
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d['nseg'] = range(1, 10)
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d['outseg'] = [4, 0, 6, 8, 3, 8, 1, 2, 8]
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return r, d
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@ -166,15 +165,13 @@ def test_sfr():
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def test_sfr_renumbering():
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# test segment renumbering
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r = np.zeros((27, 2), dtype=[('iseg', int), ('ireach', int)])
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r = np.core.records.fromarrays(r.transpose(),
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dtype=[('iseg', int), ('ireach', int)])
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dtype = [('iseg', int), ('ireach', int)]
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r = create_empty_recarray(27, dtype)
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r['iseg'] = sorted(list(range(1, 10)) * 3)
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r['ireach'] = [1, 2, 3] * 9
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d = np.zeros((9, 2), dtype=[('nseg', int), ('outseg', int)])
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d = np.core.records.fromarrays(d.transpose(),
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dtype=[('nseg', int), ('outseg', int)])
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dtype = [('nseg', int), ('outseg', int)]
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d = create_empty_recarray(9, dtype)
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d['nseg'] = range(1, 10)
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d['outseg'] = [4, 0, 6, 8, 3, 8, 1, 2, 8]
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m = flopy.modflow.Modflow()
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@ -190,9 +187,8 @@ def test_sfr_renumbering():
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r['iseg'] *= 2
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r['ireach'] = [1, 2, 3] * 9
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d = np.zeros((9, 2), dtype=[('nseg', int), ('outseg', int)])
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d = np.core.records.fromarrays(d.transpose(),
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dtype=[('nseg', int), ('outseg', int)])
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dtype = [('nseg', int), ('outseg', int)]
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d = create_empty_recarray(9, dtype)
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d['nseg'] = np.arange(1, 10) * 2
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d['outseg'] = np.array([4, 0, 6, 8, 3, 8, 1, 2, 8]) * 2
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m = flopy.modflow.Modflow()
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@ -399,12 +395,12 @@ def test_sfr_plot():
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pass
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if __name__ == '__main__':
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test_sfr()
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test_sfr_renumbering()
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test_example()
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#test_transient_example()
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#test_sfr_plot()
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#test_assign_layers()
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#test_SfrFile()
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#test_const()
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#test_sfr()
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#test_sfr_renumbering()
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#test_example()
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test_transient_example()
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test_sfr_plot()
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test_assign_layers()
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test_SfrFile()
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test_const()
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pass
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@ -122,4 +122,4 @@ def test_sfrloadcheck():
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if __name__ == '__main__':
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test_sfrcheck()
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for i, case in sfr_items.items():
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test_sfrloadcheck(i, case['mfnam'], path, cpth)
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load_check_sfr(i, case['mfnam'], path, cpth)
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@ -320,7 +320,7 @@ def test_mfnwt_LKT():
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pth = os.path.join(pthNWT, 'lkt')
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namefile = 'lkt_mf.nam'
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mf = flopy.modflow.Modflow.load(namefile, model_ws=pth,
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version='mfnwt', verbose=True,
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version='mfnwt', verbose=True, forgive=False,
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exe_name=mfnwt_exe)
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assert not mf.load_fail, 'MODFLOW model did not load'
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@ -398,5 +398,5 @@ if __name__ == '__main__':
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test_mf2000_tob()
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#test_mf2000_zeroth()
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#test_mfnwt_CrnkNic()
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#test_mfnwt_LKT()
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test_mfnwt_LKT()
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#test_mfnwt_keat_uzf()
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@ -25,7 +25,7 @@ if v is None:
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def load_str(mfnam, pth):
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m = flopy.modflow.Modflow.load(mfnam, exe_name=exe_name,
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m = flopy.modflow.Modflow.load(mfnam, exe_name=exe_name, forgive=False,
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model_ws=pth, verbose=True)
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assert m.load_fail is False
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@ -35,7 +35,7 @@ def load_lak(mfnam, pth, run):
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apth = cpth
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compth = cpth
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m = flopy.modflow.Modflow.load(mfnam, model_ws=lpth, verbose=True,
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m = flopy.modflow.Modflow.load(mfnam, model_ws=lpth, verbose=True, forgive=False,
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exe_name=exe_name)
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assert m.load_fail is False
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@ -11,6 +11,7 @@ import flopy
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import numpy as np
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from flopy.utils.reference import SpatialReference
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from flopy.utils.modpathfile import EndpointFile, PathlineFile
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from flopy.utils.recarray_utils import ra_slice
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from flopy.modpath.mpsim import StartingLocationsFile
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mffiles = glob.glob('../examples/data/mp6/EXAMPLE*')
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@ -107,7 +108,7 @@ def test_get_destination_data():
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# check that all starting locations are included in the pathline data
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# (pathline data slice not just endpoints)
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starting_locs = well_epd[['k0', 'i0', 'j0']]
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starting_locs = ra_slice(well_epd, ['k0', 'i0', 'j0'])
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pathline_locs = np.array(well_pthld[['k', 'i', 'j']].tolist(),
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dtype=starting_locs.dtype)
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assert np.all(np.in1d(starting_locs, pathline_locs))
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@ -211,6 +212,6 @@ def test_loadtxt():
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if __name__ == '__main__':
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# test_mpsim()
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test_mpsim()
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test_get_destination_data()
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# test_loadtxt()
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test_loadtxt()
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@ -35,7 +35,7 @@ def test_uzf_unit_numbers():
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apth = cpth
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compth = cpth
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m = flopy.modflow.Modflow.load(mfnam, verbose=True, model_ws=lpth,
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m = flopy.modflow.Modflow.load(mfnam, verbose=True, model_ws=lpth, forgive=False,
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exe_name=exe_name)
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assert m.load_fail is False, 'failed to load all packages'
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@ -150,4 +150,4 @@ def test_unitnums_load_and_write():
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if __name__ == '__main__':
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test_uzf_unit_numbers()
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#test_unitnums_load_and_write()
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test_unitnums_load_and_write()
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@ -5,6 +5,7 @@ import os
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import shutil
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import numpy as np
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import flopy
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from flopy.utils.recarray_utils import recarray
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cpth = os.path.join('temp', 't047')
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# delete the directory if it exists
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@ -42,9 +43,7 @@ def get_namefile_entries(fpth):
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status = status.decode()
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data.append([ftype, iu, filename, status])
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data = np.rec.array(data, dtype=dtype)
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data = recarray(data, dtype)
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return data
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def test_gage():
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@ -134,7 +134,7 @@ def test_pathline_plot():
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lpth = pth
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# load the modflow files for model map
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m = flopy.modflow.Modflow.load(mfnam, model_ws=lpth, verbose=True,
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m = flopy.modflow.Modflow.load(mfnam, model_ws=lpth, verbose=True, forgive=False,
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exe_name=mf2005_exe)
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# load modpath output files
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@ -12,7 +12,7 @@ import sys
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import numpy as np
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from ..pakbase import Package
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from ..utils.recarray_utils import create_empty_recarray
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class ModflowFhb(Package):
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"""
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@ -282,9 +282,7 @@ class ModflowFhb(Package):
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# get an empty recarray that correponds to dtype
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dtype = ModflowFhb.get_default_dtype(nbdtim=nbdtim,
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structured=structured, head=head)
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d = np.zeros((ncells, len(dtype)), dtype=dtype)
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d[:, :] = -1.0E+10
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return np.core.records.fromarrays(d.transpose(), dtype=dtype)
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return create_empty_recarray(ncells, dtype, default_value=-1.0E+10)
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@staticmethod
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def get_default_dtype(nbdtim=1, structured=True, head=False):
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@ -14,7 +14,7 @@ import numpy as np
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from ..pakbase import Package
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from ..utils import read_fixed_var, write_fixed_var
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from ..utils.recarray_utils import create_empty_recarray
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class ModflowGage(Package):
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"""
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@ -207,9 +207,7 @@ class ModflowGage(Package):
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def get_empty(ncells=0, aux_names=None, structured=True):
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# get an empty recaray that correponds to dtype
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dtype = ModflowGage.get_default_dtype()
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d = np.zeros((ncells, len(dtype)), dtype=dtype)
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d[:, :] = -1.0E+10
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return np.core.records.fromarrays(d.transpose(), dtype=dtype)
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return create_empty_recarray(ncells, dtype, default_value=-1.0E+10)
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def ncells(self):
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# Return 0 for the gage package
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@ -2,7 +2,7 @@ import sys
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import collections
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import numpy as np
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from ..pakbase import Package
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from ..utils.recarray_utils import create_empty_recarray
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# Create HeadObservation instance from a time series array
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@ -183,10 +183,9 @@ class HeadObservation(object):
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def get_empty(ncells=0):
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# get an empty recaray that correponds to dtype
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dtype = HeadObservation.get_default_dtype()
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d = np.zeros((ncells, len(dtype)), dtype=dtype)
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d[:, :] = -1.0E+10
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d[:]['obsname'] = ''
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return np.core.records.fromarrays(d.transpose(), dtype=dtype)
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d = create_empty_recarray(ncells, dtype, default_value=-1.0E+10)
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d['obsname'] = ''
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return d
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@staticmethod
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def get_default_dtype():
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@ -11,6 +11,7 @@ from ..utils import MfList
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from ..utils.flopy_io import line_parse
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import matplotlib.pyplot as plt
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from ..utils import SpatialReference
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from ..utils.recarray_utils import create_empty_recarray
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try:
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import pandas as pd
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@ -516,9 +517,7 @@ class ModflowSfr2(Package):
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dtype = ModflowSfr2.get_default_reach_dtype(structured=structured)
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if aux_names is not None:
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dtype = Package.add_to_dtype(dtype, aux_names, np.float32)
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d = np.zeros((nreaches, len(dtype)))
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d[:, :] = default_value
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d = np.core.records.fromarrays(d.transpose(), dtype=dtype)
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d = create_empty_recarray(nreaches, dtype, default_value=default_value)
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d['reachID'] = np.arange(1, nreaches + 1)
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return d
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@ -528,9 +527,8 @@ class ModflowSfr2(Package):
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dtype = ModflowSfr2.get_default_segment_dtype()
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if aux_names is not None:
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dtype = Package.add_to_dtype(dtype, aux_names, np.float32)
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d = np.zeros((nsegments, len(dtype)))
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d[:, :] = default_value
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return np.core.records.fromarrays(d.transpose(), dtype=dtype)
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d = create_empty_recarray(nsegments, dtype, default_value=default_value)
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return d
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@staticmethod
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def get_default_reach_dtype(structured=True):
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@ -1777,8 +1775,7 @@ class check:
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http://stackoverflow.com/questions/22865877/how-do-i-write-to-multiple-fields-of-a-structured-array
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"""
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txt = ''
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return txt
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array = array.copy()
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array = array.view(np.recarray).copy()
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if isinstance(col1, np.ndarray):
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array = recfunctions.append_fields(array, names='tmp1', data=col1,
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asrecarray=True)
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@ -1811,7 +1808,7 @@ class check:
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# currently failed_info[cols] results in a warning. Not sure
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# how to do this properly with a recarray.
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failed_info = recfunctions.append_fields(
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failed_info[cols].copy(),
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failed_info[cols].view(np.recarray).copy(),
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names='diff',
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data=diff,
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asrecarray=True)
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@ -12,7 +12,7 @@ import sys
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import numpy as np
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from ..utils import MfList
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from ..pakbase import Package
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from ..utils.recarray_utils import create_empty_recarray
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class ModflowStr(Package):
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"""
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@ -377,12 +377,8 @@ class ModflowStr(Package):
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dtype, dtype2 = ModflowStr.get_default_dtype(structured=structured)
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if aux_names is not None:
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dtype = Package.add_to_dtype(dtype, aux_names, np.float32)
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d = np.zeros((ncells, len(dtype)), dtype=dtype)
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d[:, :] = -1.0E+10
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d2 = np.zeros((nss, len(dtype2)), dtype=dtype2)
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d2[:, :] = 0
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return (np.core.records.fromarrays(d.transpose(), dtype=dtype),
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np.core.records.fromarrays(d2.transpose(), dtype=dtype2))
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return (create_empty_recarray(ncells, dtype=dtype, default_value=-1.0E+10),
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create_empty_recarray(nss, dtype=dtype, default_value=0))
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@staticmethod
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def get_default_dtype(structured=True):
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@ -40,3 +40,4 @@ from .zonbud import ZoneBudget, read_zbarray, write_zbarray
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from .mfgrdfile import MfGrdFile
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from .postprocessing import get_transmissivities
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from .sfroutputfile import SfrFile
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from .recarray_utils import create_empty_recarray, ra_slice
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@ -312,7 +312,6 @@ class check:
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#inds = stress_period_data[criteria][inds_col].view(int)\
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# .reshape(stress_period_data[criteria].shape + (-1,))
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if col is not None:
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v = stress_period_data[criteria][col]
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else:
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@ -9,6 +9,7 @@ important classes that can be accessed by the user.
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import numpy as np
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from ..utils.flopy_io import loadtxt
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from ..utils.recarray_utils import ra_slice
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class PathlineFile():
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"""
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@ -563,8 +564,10 @@ class EndpointFile():
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ra = self.get_alldata()
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# find the intersection of endpoints and dest_cells
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# convert dest_cells to same dtype for comparison
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raslice = ra[['k', 'i', 'j']]
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dest_cells = np.array(dest_cells, dtype=raslice.dtype)
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raslice = ra_slice(ra, ['k', 'i', 'j'])
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dest_cells = np.array(dest_cells, dtype=[('k', int),
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('i', int),
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('j', int)])
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inds = np.in1d(raslice, dest_cells)
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epdest = ra[inds].copy().view(np.recarray)
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return epdest
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@ -615,4 +618,4 @@ class EndpointFile():
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# convert back to one-based
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for n in self.kijnames:
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epd[n] += 1
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recarray2shp(epd, geoms, shpname=shpname, epsg=epsg, **kwargs)
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recarray2shp(epd, geoms, shpname=shpname, epsg=epsg, **kwargs)
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@ -0,0 +1,20 @@
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import numpy as np
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def create_empty_recarray(length, dtype, default_value=0):
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r = np.zeros(length, dtype=dtype)
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if default_value != 0:
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r[:] = default_value
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return r.view(np.recarray)
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def ra_slice(ra, cols):
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raslice = np.column_stack([ra[c] for c in cols])
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dtype = [(str(d[0]), d[1]) for d in ra.dtype.descr if d[0] in cols]
|
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return np.array([tuple(r) for r in raslice],
|
||||
dtype=dtype).view(np.recarray)
|
||||
|
||||
def recarray(array, dtype):
|
||||
# handle sequences of lists
|
||||
# (recarrays must be constructed from tuples)
|
||||
if not isinstance(array[0], tuple):
|
||||
array = list(map(tuple, array))
|
||||
return np.array(array, dtype=dtype).view(np.recarray)
|
||||
Loading…
Reference in New Issue