Skip to content

fix numpy.matrix deprecation #966

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
rieder merged 1 commit into from
Jul 6, 2023
Merged

fix numpy.matrix deprecation #966

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 26 additions & 15 deletions src/amuse/units/generic_unit_converter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,30 +73,30 @@ class ConvertBetweenGenericAndSiUnits(object):
"""

def __init__(self, *arguments_list):

self.check_arguments(arguments_list)

self.values = arguments_list

self.units_of_values = [x.unit for x in self.values]
self.system_rank = len(self.values)

self.new_base = numpy.mat(numpy.zeros((self.system_rank,self.system_rank)))
self.new_base_inv = numpy.mat(numpy.zeros((self.system_rank,self.system_rank)))
self.new_base = numpy.zeros((self.system_rank,self.system_rank))
self.new_base_inv = numpy.zeros((self.system_rank,self.system_rank))

available_units = set()
for unit in self.units_of_values:
for factor, base_unit in unit.base:
available_units.add(base_unit)
if not len(available_units) is self.system_rank:
if len(available_units) is not self.system_rank:
raise UnitsNotOrtogonalException(self.system_rank, len(available_units))
self.list_of_available_units = list(available_units)
self.list_of_available_units = numpy.array(list(available_units))

self.new_base = self.determine_new_base()
rank_of_new_base = self.matrixrank(self.new_base)
if rank_of_new_base < self.system_rank:
raise UnitsNotOrtogonalException(self.system_rank, rank_of_new_base)
self.new_base_inv = self.new_base ** -1
self.new_base_inv = numpy.linalg.matrix_power(self.new_base, -1)

def check_arguments(self, arguments):

Expand All @@ -107,25 +107,36 @@ def check_arguments(self, arguments):
raise NotAQuantityException(index, x)
if not x.is_scalar():
raise NotAScalarException(index, x)

def matrixrank(self, A, tol=1e-8):
s = numpy.linalg.svd(A,compute_uv=0)
return numpy.sum(numpy.where( s>tol, 1, 0 ) )
s = numpy.linalg.svd(A, compute_uv=0)
return numpy.sum(numpy.where(s > tol, 1, 0))

def determine_new_base(self):
matrix = numpy.asmatrix(numpy.zeros((self.system_rank,self.system_rank)))
matrix = numpy.zeros((self.system_rank, self.system_rank))
for row, value in enumerate(self.values):
for n, unit in value.unit.base:
matrix[row, [i for i, j in enumerate(self.list_of_available_units) if j == unit]] = n
matrix[
row,
[
column for column, available_unit in enumerate(
self.list_of_available_units
) if available_unit == unit
]
] = n
return matrix

@late
def conversion_factors(self):
factors_of_the_bases = numpy.asmatrix(numpy.zeros((self.system_rank,1)))
factors_of_the_bases = numpy.zeros((self.system_rank,1))
for row, value in enumerate(self.values):
factors_of_the_bases[row] = value.number * value.unit.factor
log_factors_of_the_bases = numpy.log(numpy.abs(factors_of_the_bases))
result = numpy.array(numpy.exp(self.new_base_inv*log_factors_of_the_bases))[:,0]
result = numpy.array(
numpy.exp(
numpy.matmul(self.new_base_inv, log_factors_of_the_bases)
)
)[:,0]
return result

@late
Expand All @@ -134,7 +145,7 @@ def units(self):
result = []
generic_units = mass, length, time, temperature, current, luminous_intensity

for n, unit in enumerate(self.list_of_available_units):
for n, unit in enumerate(self.list_of_available_units):
conversion_factor_for_this_base_unit = conversion_factors[n]
for generic_unit in generic_units:
if generic_unit.unit_in_si == unit:
Expand Down