Skip to content

Commit

Permalink
fix: import r runtime error
Browse files Browse the repository at this point in the history
  • Loading branch information
@statefb
statefb committed Dec 30, 2022
1 parent 318fc8e commit cb4c35d
Showing 1 changed file with 117 additions and 61 deletions.
178 changes: 117 additions & 61 deletions tests/rdtw.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,21 +3,29 @@
"""

import gc

import numpy as np
from rpy2.robjects import r
from rpy2.robjects import numpy2ri
from rpy2.robjects import pandas2ri
from rpy2.rinterface_lib.embedded import RRuntimeError
from rpy2.robjects import numpy2ri, pandas2ri, r
from rpy2.robjects.packages import importr
from rpy2.rinterface import RRuntimeError


def get_robject(result, obj_name):
for i in result.items():
if i[0] == obj_name:
return i[1]

class BaseDtw():
def __init__(self,step_pattern="symmetric2",window_type=None,window_size=None,
distance_only=False,open_end=False,open_begin=False):

class BaseDtw:
def __init__(
self,
step_pattern="symmetric2",
window_type=None,
window_size=None,
distance_only=False,
open_end=False,
open_begin=False,
):
# set parameters
self.step_pattern = step_pattern
self.window_type = window_type
Expand All @@ -31,22 +39,30 @@ def __init__(self,step_pattern="symmetric2",window_type=None,window_size=None,
raise ValueError("must specify window_size if window_type is not None.")

@staticmethod
def get_path_matrix(num_sample,path):
def get_path_matrix(num_sample, path):
"""
input:
num_sample: original ref or query number of samples (before alignment)
path: ref path or query path
"""
num_path = len(path)
D = np.zeros([num_sample,num_path])
for i,p in enumerate(path):
D[p,i] = 1
D = np.zeros([num_sample, num_path])
for i, p in enumerate(path):
D[p, i] = 1
return D


class DtwR(BaseDtw):
def __init__(self,step_pattern="symmetric2",window_type=None,window_size=10000,
distance_only=False,open_end=False,open_begin=False,rdtw=None):
def __init__(
self,
step_pattern="symmetric2",
window_type=None,
window_size=10000,
distance_only=False,
open_end=False,
open_begin=False,
rdtw=None,
):
self.step_pattern = step_pattern
self.window_type = window_type
self.window_size = window_size
Expand All @@ -67,68 +83,108 @@ def __init__(self,step_pattern="symmetric2",window_type=None,window_size=10000,
pandas2ri.activate()

# set window type if it's none
if self.window_type is None: self.window_type = "none"
if self.window_type is None:
self.window_type = "none"

def fit(self,global_cost_matrix):
def fit(self, global_cost_matrix):
# set params to R environment
r.assign("window.type",self.window_type)
r.assign("window.size",self.window_size)
r.assign("step.pattern",DtwR._get_r_step_pattern(self._rdtw,self.step_pattern))
r.assign("open.begin",self.open_begin)
r.assign("open.end",self.open_end)
r.assign("distance.only",self.distance_only)
r.assign("lm",global_cost_matrix)
r.assign("window.type", self.window_type)
r.assign("window.size", self.window_size)
r.assign(
"step.pattern", DtwR._get_r_step_pattern(self._rdtw, self.step_pattern)
)
r.assign("open.begin", self.open_begin)
r.assign("open.end", self.open_end)
r.assign("distance.only", self.distance_only)
r.assign("lm", global_cost_matrix)
try:
res_dtw = r("dtw(lm,keep.internals=T,window.type=window.type,\
res_dtw = r(
"dtw(lm,keep.internals=T,window.type=window.type,\
distance.only=distance.only,window.size=window.size,\
step.pattern=step.pattern,open.begin=open.begin,open.end=open.end)")
step.pattern=step.pattern,open.begin=open.begin,open.end=open.end)"
)
except RRuntimeError as e:
print("An exception occurred in rdtw package: " + e.args[0])
raise

gc.collect()

self.distance = np.array(get_robject(res_dtw,"distance"))[0]
self.normalized_distance = np.array(get_robject(res_dtw,"normalizedDistance"))[0]
self.distance = np.array(get_robject(res_dtw, "distance"))[0]
self.normalized_distance = np.array(get_robject(res_dtw, "normalizedDistance"))[
0
]
if not self.distance_only:
self.ref_path = np.array(res_dtw[13],dtype="int") - 1
self.ref_path = np.array(res_dtw[13], dtype="int") - 1
self.ref_path_matrix = BaseDtw.get_path_matrix(
global_cost_matrix.shape[1],self.ref_path)
self.query_path = np.array(res_dtw[12],dtype="int") - 1
global_cost_matrix.shape[1], self.ref_path
)
self.query_path = np.array(res_dtw[12], dtype="int") - 1
self.query_path_matrix = BaseDtw.get_path_matrix(
global_cost_matrix.shape[0],self.query_path)
self.ref_warp_index = np.array(self._rdtw.warp(res_dtw,True),dtype="int") - 1
self.query_warp_index = np.array(self._rdtw.warp(res_dtw,False),dtype="int") - 1
self.cumsum_matrix = np.array(get_robject(res_dtw,"costMatrix"))
global_cost_matrix.shape[0], self.query_path
)
self.ref_warp_index = (
np.array(self._rdtw.warp(res_dtw, True), dtype="int") - 1
)
self.query_warp_index = (
np.array(self._rdtw.warp(res_dtw, False), dtype="int") - 1
)
self.cumsum_matrix = np.array(get_robject(res_dtw, "costMatrix"))

return self

@staticmethod
def _get_r_step_pattern(rdtw,step_pattern_str):
if step_pattern_str == "symmetric2":return rdtw.symmetric2
elif step_pattern_str == "symmetric1":return rdtw.symmetric1
elif step_pattern_str == "symmetricP05":return rdtw.symmetricP05
elif step_pattern_str == "symmetricP2":return rdtw.symmetricP2
elif step_pattern_str == "symmetricP0":return rdtw.symmetricP0
elif step_pattern_str == "symmetricP1":return rdtw.symmetricP1
elif step_pattern_str == "asymmetric":return rdtw.asymmetric
elif step_pattern_str == "asymmetricP0":return rdtw.asymmetricP0
elif step_pattern_str == "asymmetricP05":return rdtw.asymmetricP05
elif step_pattern_str == "asymmetricP2":return rdtw.asymmetricP2
elif step_pattern_str == "asymmetricP1":return rdtw.asymmetricP1
elif step_pattern_str == "typeIa":return rdtw.typeIa
elif step_pattern_str == "typeIb":return rdtw.typeIb
elif step_pattern_str == "typeIc":return rdtw.typeIc
elif step_pattern_str == "typeId":return rdtw.typeId
elif step_pattern_str == "typeIas":return rdtw.typeIas
elif step_pattern_str == "typeIbs":return rdtw.typeIbs
elif step_pattern_str == "typeIcs":return rdtw.typeIcs
elif step_pattern_str == "typeIds":return rdtw.typeIds
elif step_pattern_str == "typeIIa":return rdtw.typeIIa
elif step_pattern_str == "typeIIb":return rdtw.typeIIb
elif step_pattern_str == "typeIIc":return rdtw.typeIIc
elif step_pattern_str == "typeIId":return rdtw.typeIId
elif step_pattern_str == "typeIIIc":return rdtw.typeIIIc
elif step_pattern_str == "typeIVc":return rdtw.typeIVc
elif step_pattern_str == "mori2006":return rdtw.mori2006
else:raise NotImplementedError()
def _get_r_step_pattern(rdtw, step_pattern_str):
if step_pattern_str == "symmetric2":
return rdtw.symmetric2
elif step_pattern_str == "symmetric1":
return rdtw.symmetric1
elif step_pattern_str == "symmetricP05":
return rdtw.symmetricP05
elif step_pattern_str == "symmetricP2":
return rdtw.symmetricP2
elif step_pattern_str == "symmetricP0":
return rdtw.symmetricP0
elif step_pattern_str == "symmetricP1":
return rdtw.symmetricP1
elif step_pattern_str == "asymmetric":
return rdtw.asymmetric
elif step_pattern_str == "asymmetricP0":
return rdtw.asymmetricP0
elif step_pattern_str == "asymmetricP05":
return rdtw.asymmetricP05
elif step_pattern_str == "asymmetricP2":
return rdtw.asymmetricP2
elif step_pattern_str == "asymmetricP1":
return rdtw.asymmetricP1
elif step_pattern_str == "typeIa":
return rdtw.typeIa
elif step_pattern_str == "typeIb":
return rdtw.typeIb
elif step_pattern_str == "typeIc":
return rdtw.typeIc
elif step_pattern_str == "typeId":
return rdtw.typeId
elif step_pattern_str == "typeIas":
return rdtw.typeIas
elif step_pattern_str == "typeIbs":
return rdtw.typeIbs
elif step_pattern_str == "typeIcs":
return rdtw.typeIcs
elif step_pattern_str == "typeIds":
return rdtw.typeIds
elif step_pattern_str == "typeIIa":
return rdtw.typeIIa
elif step_pattern_str == "typeIIb":
return rdtw.typeIIb
elif step_pattern_str == "typeIIc":
return rdtw.typeIIc
elif step_pattern_str == "typeIId":
return rdtw.typeIId
elif step_pattern_str == "typeIIIc":
return rdtw.typeIIIc
elif step_pattern_str == "typeIVc":
return rdtw.typeIVc
elif step_pattern_str == "mori2006":
return rdtw.mori2006
else:
raise NotImplementedError()

0 comments on commit cb4c35d

Please sign in to comment.