1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
|
"""
The data provided with these dataset have been kindly made
available by several ESRF scientists.
Thanks to Paul , Wolfgang and Paola .
If you reuse those provided in PATCHES_VECTORIAL
you are kindly asked to aknoweledge the following
collaboration
"We acknowledge the German Excellence cluster "Munich-centre for Advanced Photonics" (EXC158),
the Department of Clinical Radiology of the Ludwig Maximilians University (Munich) and
the Biomedical beamline of the ESRF (Grenoble) for the provision of experimental data."
To run all them all you have to do is
python nonregression.py
provided that you did the following , beforehand :
you have to change three prefix,
the lanching instruction for pyhst2 (LAUNCHING_INSTRUCTION),
and optinally set the mailserver variable of you want to be notified by mail of the tasks end:
The prefixs :
--- outputprefix : the several reconstructed cases, you will find them in an arborescence
starting at outputprefix
--- inputprefix : all the input.par files in the arborescence below inputprefix will be runned
--- PREFIX : this is where the data set are.
The available cases are
CASI = [ "NNFBP","CRAYON" , "MULTIPAGANIN", "PATCHES_VECTORIAL", "LENA_MULTIRINGS", "ID11_SNOW", "SIRT_LENA" ]
You can run shorter tests by shortening such list.
"""
mailserver = None
# mailserver="tuodomain.country"
# LAUNCHING_INSTRUCTION = "echo 'localhost\n' > machinefile ; time PyHST2_2017c input.par gpu2-1304,0"
# LAUNCHING_INSTRUCTION = "time PyHST2_2018b input.par scisoft13,0 | tee output"
# outputprefix="/data/scisofttmp/mirone/TEST_PYHST/RESULTS/2017c/2gpu_bis/tests"
# outputprefix="/data/scisofttmp/paleo/TEST_PYHST/DATASETS_RED/OUTPUTS"
inputprefix ="INPUTS"
CASI_DISTRIBUTED = ["NNFBP", "CRAYON", "ID11_SNOW", "LENA_MULTIRINGS", "MULTIPAGANIN", "PATCHES_VECTORIAL", "SIRT_LENA"]
CASI_ALL = [ "BIG", "CRAYON", "HEIKKI", "HELICOIDAL", "ID11_SNOW", "LENA", "LENA_MULTIRINGS", "MOUSSE", "MULTIPAGANIN","NANOPOINTS", "NNFBP",
"PATCHES_VECTORIAL", "SINO_THRESHOLD", "SIRT_LENA" ]
CASI_partial = [ "ID11_SNOW", "LENA", "LENA_MULTIRINGS", "MOUSSE", "MULTIPAGANIN","NANOPOINTS", "NNFBP",
"PATCHES_VECTORIAL", "SINO_THRESHOLD", "SIRT_LENA" ]
casi = [ "LENA", "LENA_MULTIRINGS", "MOUSSE", "MULTIPAGANIN","NANOPOINTS", "PATCHES_VECTORIAL", "SINO_THRESHOLD", "SIRT_LENA" ]
##################################################
PREFIX="/home/esrf/mirone/WORKS/TEST_PYHST/DATASETS"
casi=[ "CRAYON", "HEIKKI", "HELICOIDAL", "ID11_SNOW", "LENA", "LENA_MULTIRINGS", "MOUSSE", "MULTIPAGANIN","NANOPOINTS",
"PATCHES_VECTORIAL", "SINO_THRESHOLD" ]
casi=["ID11_SNOW", "BIG", "LENA", "LENA_MULTIRINGS", "MOUSSE", "MULTIPAGANIN","NANOPOINTS", "PATCHES_VECTORIAL", "SINO_THRESHOLD"]
LAUNCHING_INSTRUCTION = "PyHST2_2020c input.par"
outputprefix="/home/esrf/mirone/nobackup/TEST_PYHST/RESULTS/p9/monogpu"
# outputprefix="/tmp/TEST_PYHST/RESULTS/p9-04/"
###############################################################
import fnmatch
import os
import shutil
import string
ADATTA_INPUT=0
def adapt(l, prefix):
pos = l.find("#")
if pos>=0:
l=l[:pos]
pos = l.find("prefix")
if pos==-1:
return l
if l[pos-1] in [" ","="] and l[pos+6] in [" ","+" ]:
pos1 = l.find("\"")
pos2 = pos1+1+l[pos1+1:].find("\"")
l = l[:pos] + prefix + l[pos1+1:pos2]
return l
def getprefix(l):
if "prefix"==l[:6]:
exec(l)
return prefix
def lancia_comando():
#os.system("PyHST2_eli input.par scisoft12,0")
if not ADATTA_INPUT:
# os.system("echo 'localhost\nlocalhost\nlocalhost\nlocalhost\n' > machinefile ; time PyHST2_2015d input.par gpu3-1801,0,1,2,3 | tee log.out")
# os.system("echo 'localhost\n' > machinefile ; time PyHST2_2015d input.par gpu3-1801,7")
# os.system("echo 'localhost\n' > machinefile ; time PyHST2_2015d input.par scisoft11,0")
os.system( LAUNCHING_INSTRUCTION )
# os.system("pyhst_2_2015d input.par")
# os.system("pyhst_2_2015f input.par gpu2-1403,0")
# os.system("PyHST2_2015f input.par 2>stderr.log 1>stdlog.log ") #command 2> error 1> output
# os.system("PyHST2_2015d input.par ")
else:
# os.system("PyHST2_2015b input_adapted.par")
os.system("pyhst2 input.par")
matches = []
for root, dirnames, filenames in os.walk(inputprefix):
for filename in fnmatch.filter(filenames, 'input.par'):
matches.append(os.path.join(root, filename))
repertori = []
tmpmatches = matches
matches=[]
for caso in casi:
for inp in tmpmatches:
inpcut = inp[len(inputprefix)+1:]
pL = inpcut.find("/")
inpcut = inpcut[:pL]
if inpcut == caso:
matches.append(inp)
for inp in matches:
print( inp)
pL = inp.find("/")
pR = inp.rfind("/")
direttorio = os.path.join(outputprefix,inp[pL+1:pR])
filename = inp[pR+1:]
print( direttorio)
print( filename)
if not os.path.exists(direttorio):
os.makedirs(direttorio)
shutil.copy2(inp, os.path.join( direttorio , filename ))
repertori.append(direttorio)
repertori.sort()
for d in repertori:
savedPath = os.getcwd()
os.chdir(d)
if ADATTA_INPUT:
S=""
s=string.split(open("input.par","r").read(),"\n")
gotprefix=0
for l in s:
if not gotprefix:
prefix = getprefix(l)
if prefix is not None:
gotprefix=1
continue
if gotprefix:
l=adapt(l, prefix)
S=S+l+"\n"
open("input_adapted.par","w").write(S)
print( S)
if(1):
s=open("input.par","r").read()
s="PREFIX=\"%s\" \n"%PREFIX +s
open("input.par","w").write(s)
lancia_comando()
os.chdir(savedPath)
def send_mail():
if mailserver is not None:
to = os.environ.get("USER").lower() + "@%s" %mailserver
os.system("echo 'This is a notification that the reconstruction is done. The results are stored in " + str(savedPath) + "' | mail -s 'PyHST2 end of job notification' " + to)
send_mail()
|
