Refs #76. slight refactor: added shutils.exec_redirect_to_stdout and …

…use it in mpi filter and mpi reconstruction

python/imars3d/decorators.py

@@ -62,17 +62,8 @@ def _(*args, **kwds):
         for k,v in kwds.items():
             logger.info("    - %s: %s" % (k,v))
             continue
-        import subprocess as sp, shlex, sys
-        args = shlex.split(cmd)
-        # sp.check_call(args, shell=False)
-        # manually pipe the output from the subprocess to sys.stdout so that
-        # jupyter gets it inside the web page instead of the stdout of the terminal
-        # from which jupyter is launched
-        p = sp.Popen(args, shell=False, stdout=sp.PIPE, stderr=sp.STDOUT)
-        for c in iter(lambda: p.stdout.read(1), ''):
-            sys.stdout.write(c)
-        p.communicate(); r = p.poll()
-        if r: raise RuntimeError("Cmd %r failed" % cmd)
+        from .shutils import exec_redirect_to_stdout
+        exec_redirect_to_stdout(cmd)
         logger.info("done.")
         return
     return _

python/imars3d/jnbui/tomoreconui.py

@@ -176,7 +176,7 @@ def nextStep(self):
         """
         Removes the current panel. Then, creates a ct object,
         and saves it into context's ct member.
-        Fianlly, creates an ImgSliderPanel and displays it.
+        Fianlly, creates an MainUIPanel and displays it.
         """
         self.remove()
         from imars3d.CT import CT
@@ -186,7 +186,7 @@ def nextStep(self):
                 outdir=context.config.outdir, ob_files=context.config.ob_files,
                 df_files=context.config.df_files)
         context.ct = ct
-        img_slide = ImgSliderPanel(context)
+        img_slide = MainUIPanel(context)
         img_slide.show()
 
 
@@ -342,7 +342,7 @@ def nextStep(self):
         Then, after printing the configuration, creates a ct object,
         and stores the result in context.ct. 
         Finally, removes the current panel,
-        and replaces it with an ImgSliderPanel.
+        and replaces it with an MainUIPanel.
         """
         # save path of current imars3d config
         import imars3d;  orig_imars3d_config = os.path.abspath(imars3d.conf_path)
@@ -377,11 +377,11 @@ def nextStep(self):
         context.ct = ct
         # new interface
         self.remove()
-        imgslide = ImgSliderPanel(context)
+        imgslide = MainUIPanel(context)
         imgslide.show()
 
 
-class ImgSliderPanel(base.Panel):
+class MainUIPanel(base.Panel):
     """Creates a tab interface where each tab displays
        an ImageSlider widget with either the CT, DF, or OB
        images displayed. In each tab, there is also
@@ -390,9 +390,11 @@ class ImgSliderPanel(base.Panel):
        a new tab is added that displays
        an ImageSlider of the reconstructed images."""
 
+    layout = ipyw.Layout(border="1px solid lightgray", padding='4px')
+
     def __init__(self, context):
         """
-        Create ImgSliderPanel instance.
+        Create MainUIPanel instance.
         
         Parameters
         ----------
@@ -407,9 +409,9 @@ def __init__(self, context):
         with wait_alert("Preprocessing. Please wait..."):
             self.ppd = ct.preprocess()
         # create interface
-        explanation = ipyw.Label(
-            "Select a Region of Interest from the CT Images, and make sure the OB and DF images are reasonable",
-            layout = ipyw.Layout(height='35px', padding='4px', width='500px')
+        explanation = ipyw.HTML(
+            "<p>Select a Region of Interest from the CT Images, and make sure the OB and DF images are reasonable</p>",
+            layout = ipyw.Layout(padding='4px', width='500px')
             )
         # image sliders
         self.ct_slider = ImgSlider.ImageSlider(self.ppd, self.width, self.height)
@@ -432,7 +434,7 @@ def __init__(self, context):
         self.recon_button = ipyw.Button(description="Reconstruct", layout=self.button_layout)
         self.recon_button.on_click(self.onRecon)
         # 
-        self.panel = ipyw.VBox(children=[explanation, self.tabs, self.recon_button])
+        self.panel = ipyw.VBox(children=[explanation, self.tabs, self.recon_button], layout=self.layout)
         return
 
     def onRecon(self, event):

python/imars3d/recon/mpi.py

@@ -44,8 +44,8 @@ def recon(sinograms, theta, recon_series, nodes=None, **kwds):
     nodes = min(nodes, imars3d.configuration['parallelization']['max_nodes'])
     # shell cmd
     cmd = 'mpirun -np %(nodes)s python %(pyfile)s' % locals()
-    if os.system(cmd):
-        raise RuntimeError("%s failed" % cmd)
+    from ..shutils import exec_redirect_to_stdout
+    exec_redirect_to_stdout(cmd)
     return
 
 

python/imars3d/shutils.py

@@ -1,4 +1,19 @@
 
+def exec_redirect_to_stdout(cmd, shell=False):
+    "execute a command in a subproces and redirect outputs (including errors) to sys.stdout"
+    import subprocess as sp, shlex, sys
+    args = shlex.split(cmd)
+    # sp.check_call(args, shell=shell)
+    # manually pipe the output from the subprocess to sys.stdout so that
+    # jupyter gets it inside the web page instead of the stdout of the terminal
+    # from which jupyter is launched
+    p = sp.Popen(args, shell=shell, stdout=sp.PIPE, stderr=sp.STDOUT)
+    for c in iter(lambda: p.stdout.read(1), ''):
+        sys.stdout.write(c)
+    p.communicate(); r = p.poll()
+    if r: raise RuntimeError("Cmd %r failed" % cmd)
+    return
+
 
 def exec_withlog(cmd, logfile):
     import subprocess as sp, shlex