making run scripts independent of calling directory

regression/devtests/LIMPET/em_coupling/run.py

@@ -14,14 +14,12 @@ Following optional arguments with their default values are available:
     ./run.py --model=MBRDR
     ./run.py --list
 """
+import os, sys
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Electromechanical Single Cell Stretcher'
 EXAMPLE_AUTHOR = 'Gernot Plank <gernot.plank@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
-import math
-import subprocess
 import numpy as np
 from datetime import date
 from matplotlib import pyplot

regression/devtests/LIMPET/ionic_model/run.py

@@ -17,9 +17,6 @@ Following optional arguments with their default values are available:
 
 from __future__ import print_function
 import os
-import sys
-import math
-import subprocess
 import numpy as np
 from datetime import date
 
@@ -30,6 +27,7 @@ from carputils import tools
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Isolated Ionic Model'
 EXAMPLE_AUTHOR = 'Anton Prassl <anton.prassl@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
 MODEL_EXCLUDE_LIST = ['IION_SRC', 'UCLA_RAB_SCR']
 

regression/devtests/LIMPET/plugin/run.py

@@ -17,9 +17,6 @@ Following optional arguments with their default values are available:
 
 from __future__ import print_function
 import os
-import sys
-import math
-import subprocess
 import numpy as np
 from datetime import date
 
@@ -32,6 +29,7 @@ from carputils import divertoutput
 EXAMPLE_DESCRIPTIVE_NAME = 'LIMPET Plugins'
 EXAMPLE_AUTHOR = ('Anton Prassl <anton.prassl@medunigraz.at> and '
                   'Andrew Crozier <andrew.crozier@medunigraz.at>')
+EXAMPLE_DIR = os.path.dirname(__file__)
 
 AXIS_LABEL = {'Tension': 'Tension (kPa)'}
 
@@ -43,7 +41,7 @@ def parser():
                         default='LR1',
                         help='select IMP model')
     group.add_argument('--plugin',
-                        default='FxStress',
+                        default='LandStress',
                         help='select LIMPET plugin')
     group.add_argument('--param', '-p',
                         nargs=2, action='append',

regression/devtests/bidomain/cable_1D/run.py

@@ -3,12 +3,12 @@
 """
 One dimensional cable EP simulation.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = '1D Cable Bidomain'
 EXAMPLE_AUTHOR = 'Unassigned'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -16,6 +16,7 @@ from carputils import tools
 from carputils import mesh
 from carputils import testing
 
+
 def parser():
     parser = tools.standard_parser()
     parser.add_argument('--spacing',
@@ -50,7 +51,7 @@ def run(args, job):
     geom.generate_carp(meshname)
 
     # Get basic command line, including solver options
-    cmd = tools.carp_cmd('cable_1D.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'cable_1D.par'))
 
     cmd += ['-simID',    job.ID,
             '-meshname', meshname]
@@ -64,7 +65,7 @@ def run(args, job):
         # Prepare file paths
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'vm.igb.gz')
-        view = 'cable_1D.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'cable_1D.mshz')
         
         # Call meshalyzer
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/checkpoint/run.py

@@ -3,12 +3,12 @@
 """
 Demonstration and testing of checkpointing and restarting CARP.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Checkpoint and Restart'
 EXAMPLE_AUTHOR = 'Gernot Plank <gernot.plank@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -63,7 +63,7 @@ def run(args, job):
     meshname = mesh.generate(geom)
 
     # define default view settings
-    view = 'checkpoint.mshz'
+    view = os.path.join(EXAMPLE_DIR, 'checkpoint.mshz')
  
     # Simulation output directories
     chkID = job.ID
@@ -73,7 +73,7 @@ def run(args, job):
         rstID = os.path.join(job.ID, 'restart')
 
     # Add all the non-general arguments
-    cmd = tools.carp_cmd('checkpoint.par')
+    cmd  = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'checkpoint.par'))
     cmd += ['-meshname', meshname]
 
     if args.visualize:
@@ -103,7 +103,7 @@ def run(args, job):
 
         geom = os.path.join(chkID, os.path.basename(meshname)+'_i')
         data = os.path.join(chkID, 'vm.igb')
-        view = 'checkpoint.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'checkpoint.mshz')
         
         job.gunzip(data)
         job.meshalyzer(geom, data, view)
@@ -111,7 +111,7 @@ def run(args, job):
         if args.experiment == 'restart':
             geom = os.path.join(rstID, os.path.basename(meshname)+'_i')
             data = os.path.join(rstID, 'vm.igb')
-            view = 'restart.mshz'
+            view = os.path.join(EXAMPLE_DIR, 'restart.mshz')
         
             job.gunzip(data)
             job.meshalyzer(geom, data, view)

regression/devtests/bidomain/ecg/run.py

@@ -7,12 +7,12 @@ The wedge contains transmural (Boukens et al. Cardiovasc Res 2015) as well as ap
 .. image:: /images/ecg_setup.png
     :scale: 60%
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'ECG simulation on a tissue wedge with heterogeneity'
 EXAMPLE_AUTHOR = 'Fernando Campos <fernando.campos@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -240,7 +240,7 @@ def run(args, job):
            '-lats[0].method', 1]
     
     # ECG
-    ecg = ['-phie_rec_ptf','ecg',
+    ecg = ['-phie_rec_ptf', os.path.join(EXAMPLE_DIR, 'ecg'),
            '-dump_ecg_leads', 1]
 
 
@@ -272,7 +272,7 @@ def run(args, job):
         # Prepare file paths
         geom = os.path.join(simID, os.path.basename(meshname)+'_i')
         data = os.path.join(simID, 'vm.igb')
-        view = 'view.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'view.mshz')
         
         # Call meshalyzer to show Vm
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/laplace/run.py

@@ -3,12 +3,12 @@
 """
 Demonstration of solving Laplace's equation in CARP.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Laplace\'s Equation'
 EXAMPLE_AUTHOR = 'Andrew Crozier <andrew.crozier@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -87,7 +87,7 @@ def run(args, job):
         # Prepare file paths
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'phie.igb.gz')
-        view = 'laplace.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'laplace.mshz')
         
         # Call meshalyzer
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/lats/run.py

@@ -3,12 +3,12 @@
 """
 Compute activation times from bidomain simulation.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Activation Time Computation'
 EXAMPLE_AUTHOR = 'Gernot Plank <gernot.plank@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 import numpy as np
 from datetime import date
 
@@ -237,7 +237,7 @@ def run(args, job):
     lat = LATDetector(args.measurand, args.method, args.event, args.all)
 
     # Add all the non-general arguments
-    cmd = tools.carp_cmd('lats.par')
+    cmd = tools.carp_cmd(os.path.join(os.path.dirname(__file__), 'lats.par'))
 
     cmd += ['-simID',    job.ID,
             '-meshname', meshname,
@@ -279,7 +279,7 @@ def run(args, job):
             # choosing the first
             data = os.path.join(job.ID, 'all_lats_0')
 
-        view = 'lats.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'lats.mshz')
         
         job.meshalyzer(geom, data, view)
 

regression/devtests/bidomain/noground_bidom/run.py

@@ -3,12 +3,12 @@
 """
 Description TBD.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Bidomain without a Ground-type Stimulus'
 EXAMPLE_AUTHOR = 'Aurel Neic <aurel.neic@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -49,7 +49,7 @@ def run(args, job):
     meshname = mesh.generate(geom)
 
     # Add all the non-general arguments
-    cmd = tools.carp_cmd('noground-bidom.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'noground-bidom.par'))
     cmd += tools.gen_physics_opts(ExtraTags=[0, 1], IntraTags=[1])
 
     cmd += ['-meshname', meshname,
@@ -78,7 +78,7 @@ def run(args, job):
 
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'phie_i.igb.gz')
-        view = 'view_phie.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'view_phie.mshz')
 
         job.meshalyzer(geom, data, view)
 

regression/devtests/bidomain/phie_recovery/run.py

@@ -32,8 +32,8 @@ the results in meshalyzer:
 
     ./run.py --visualize
 """
-
-import os, sys
+import os
+import sys
 import numpy as np
 from datetime   import date
 from shutil     import copyfile
@@ -47,7 +47,7 @@ from carputils import tools
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Phie Recovery'
 EXAMPLE_AUTHOR = 'Anton Prassl <anton.prassl@medunigraz.at>'
-
+EXAMPLE_DIR = os.path.dirname(__file__)
 
 isPy2 = True
 if sys.version_info.major > 2:
@@ -141,7 +141,7 @@ def plot_traces(job, sourceModel, phieFile):
 
     geomfile = os.path.join(job.ID, 'block_i')
     datafile = os.path.join(job.ID, 'vm.igb')
-    view     = 'vm_view.mshz'
+    view     = os.path.join(EXAMPLE_DIR, 'vm_view.mshz')
 
     # Call meshalyzer
     job.meshalyzer(geomfile, datafile, view)
@@ -203,7 +203,7 @@ def run(args, job):
 
 
     # Get basic command line, including solver options
-    cmd = tools.carp_cmd('carp.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'carp.par'))
 
     # determine model type
     cmd += ep.model_type_opts(args.sourceModel)

regression/devtests/bidomain/prepace/run.py

@@ -3,12 +3,12 @@
 """
 Description TBD.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Prepace'
 EXAMPLE_AUTHOR = 'Fernando Campos <fernando.campos@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings

regression/devtests/bidomain/region_vs_gradient_based_heterogeneities/run.py

@@ -119,12 +119,12 @@ be seen using the --visualize function:
     repolarisation heterogeneity
 
 """
+import os, sys
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Region- vs. Gradient-Based Heterogeneities'
 EXAMPLE_AUTHOR = 'Patrick Boyle <pmjboyle@gmail.com>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 import numpy as np
 from datetime import date
 
@@ -247,7 +247,7 @@ def run(args, job):
 
     # setup command line and run simulation #1 (Region-wise APD variability)
     simID1 = os.path.join(job.ID, 'RegionWise_{0:4.2f}-{1:4.2f}'.format(f_min_scf,f_max_scf))
-    cmd    = tools.carp_cmd('Region-Wise-APD-Variability.par')
+    cmd    = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'Region-Wise-APD-Variability.par'))
     cmd   += ['-simID',                  simID1,
               '-tend',                   args.duration,
               '-imp_region[0].im_param', reg0_cmd,
@@ -312,7 +312,7 @@ def run(args, job):
 
     # Setup command line and run simulation #2 (Gradient-wise APD variability)
     simID2 = os.path.join(job.ID, 'GradientWise_{0:4.2f}-{1:4.2f}'.format(f_min_scf,f_max_scf))
-    cmd    = tools.carp_cmd('Gradient-Wise-APD-Variability.par')
+    cmd    = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'Gradient-Wise-APD-Variability.par'))
     cmd   += ['-simID',              simID2,
               '-tend',               args.duration,
               '-adjustment[0].file', adjf_gKr_fn + '.adj',
@@ -348,7 +348,7 @@ def run(args, job):
     if args.visualize and not settings.platform.BATCH:
         geom = meshname
         data = dAPD_fn
-        view = 'DeltaAPD.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'DeltaAPD.mshz')
         job.meshalyzer(geom, data, view)
 
 

regression/devtests/bidomain/resistor/run.py

@@ -34,12 +34,12 @@ which can be set to extra_V or extra_I.
     ./run.py --stimulus extra_I
 
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'resistor'
 EXAMPLE_AUTHOR = 'Gernot Plank <gernot.plank@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -103,7 +103,7 @@ def run(args, job):
         raise Exception('Unknown stimulus type!')
 
     # Add all the non-general arguments
-    cmd = tools.carp_cmd('resistor.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'resistor.par'))
 
     cmd += ['-meshname',  meshname,
             '-gridout_i', 3,
@@ -127,7 +127,7 @@ def run(args, job):
 
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'phie.igb')
-        view = 'resistor.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'resistor.mshz')
         
         job.gunzip(data)
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/scr/run.py

@@ -7,12 +7,12 @@ The strand contains transmural (Boukens et al. Cardiovasc Res 2015) as well as a
 .. image:: /images/ecg_setup.png
     :scale: 60%
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'SCR-mediated ectopy'
 EXAMPLE_AUTHOR = 'Fernando Campos <fernando.campos@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -62,7 +62,8 @@ def run(args, job):
     imp_reg = ['-num_imp_regions', 1,
                '-imp_region[0].im', 'UCLA_RAB_SCR',
                '-imp_region[0].im_param', 'g_K1*0.3,i_NaCamax*2.0,Ca_o*2.7,CSR=1600',
-               '-imp_region[0].im_sv_init','UCLA_RAB_SCR_DAD_CSR_1600uM_100npls_400bcl_INIT.st']
+               '-imp_region[0].im_sv_init',os.path.join(EXAMPLE_DIR,
+                                                        'UCLA_RAB_SCR_DAD_CSR_1600uM_100npls_400bcl_INIT.st')]
 
     # TISSUE SETUP
     g_reg = ['-bidomain',0,
@@ -79,7 +80,7 @@ def run(args, job):
     # NOTE: here we provide seeds for the random number generator (without them you can't reproduce a simulation)
     imp_adj = ['-num_adjustments', 1,
                '-adjustment[0].variable', 'UCLA_RAB_SCR.seed',
-               '-adjustment[0].file', 'Cardiac-Strand.seeds']
+               '-adjustment[0].file', os.path.join(EXAMPLE_DIR, 'Cardiac-Strand.seeds')]
 
     # NO STIMULUS
     stim = ['-num_stim', 0]
@@ -128,7 +129,7 @@ def run(args, job):
         # Prepare file paths
         geom = os.path.join(simID, os.path.basename(meshname)+'_i')
         data = os.path.join(simID, 'vm.igb')
-        view = 'view.mshz'
+        view = '' #os.path.join(EXAMPLE_DIR, 'view.mshz')
 
         # Call meshalyzer to show Vm
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/simple/run.py

@@ -44,11 +44,12 @@ the results in meshalyzer:
 
     ./run.py --tend 100 --visualize
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Simple Bidomain Example'
 EXAMPLE_AUTHOR = 'Andrew Crozier <andrew.crozier@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
 from datetime import date
 
 from carputils import settings
@@ -88,7 +89,7 @@ def run(args, job):
     stim = mesh.block_bc_opencarp(geom, 'stim', 0, 'x', False)
 
     # Get basic command line, including solver options
-    cmd = tools.carp_cmd('simple.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'simple.par'))
     cmd += tools.gen_physics_opts(ExtraTags=[0, 1], IntraTags=[1])
 
     cmd += ['-simID',    job.ID,
@@ -109,7 +110,7 @@ def run(args, job):
         # Prepare file paths
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'vm.igb.gz')
-        view = 'simple.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'simple.mshz')
 
         # Call meshalyzer
         job.meshalyzer(geom, data, view)

regression/devtests/bidomain/stimulation/run.py

@@ -50,12 +50,12 @@ Optional Arguments
    in this case which essentially enforces the integral over the extracellular potential
    to be zero at each instant in time, but no specific point is clamped.
 """
+import os
 
 EXAMPLE_DESCRIPTIVE_NAME = 'Stimulation'
 EXAMPLE_AUTHOR = 'Gernot Plank <gernot.plank@medunigraz.at>'
+EXAMPLE_DIR = os.path.dirname(__file__)
 
-import os
-import sys
 from datetime import date
 
 from carputils import settings
@@ -107,7 +107,7 @@ def run(args, job):
     mod  = []
 
     # define default view settings
-    view = 'stimulation_V.mshz'
+    view = os.path.join(EXAMPLE_DIR, 'stimulation_V.mshz')
 
     # make subtest specific settings
     if args.stimulus == 'extra_V':
@@ -173,7 +173,7 @@ def run(args, job):
         raise Exception('Unknown stimulus type!')
 
     # Add all the non-general arguments
-    cmd = tools.carp_cmd('stimtest.par')
+    cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'stimtest.par'))
     cmd += tools.gen_physics_opts(ExtraTags=[0, 1], IntraTags=[1])
 
     cmd += ['-meshname',  meshname,
@@ -197,7 +197,7 @@ def run(args, job):
 
         geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
         data = os.path.join(job.ID, 'phie.igb')
-        view = 'stimulation.mshz'
+        view = os.path.join(EXAMPLE_DIR, 'stimulation.mshz')
 
         job.gunzip(data)
         job.meshalyzer(geom, data, view)