Debugging - Real case use

CHANGELOG

@@ -6,6 +6,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.0] - 2021-06-04
+### Added
+- None 
+
+### Changed
+- Use pickle5 to save data
+
+### Removed
+- None
+
 ## [0.1.2] - 2020-10-29
 ### Added
 - add OrderedDict() function to keep input ordered independent to Python version 
@@ -149,4 +159,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - None
 
 ### Removed
-- None
\ No newline at end of file
+- None

tooba_f.py

@@ -3,11 +3,12 @@ import numpy as np
 #from mpl_toolkits.mplot3d import Axes3D
 import matplotlib.pyplot as plt
 import scipy.optimize
-import pickle as pkl
+import pickle5 as pkl
 import json
 import re
 import pandas as pd
 from progress.bar import Bar
+import joblib
 
 from pytrr import (
     read_trr_header,
@@ -66,15 +67,47 @@ def center_gravity(a):
     cg = np.sum(a)/m
     return cg
 
+class StreamFile(object):
+    def __init__(self, f):
+        self.f = f
+    def __getattr__(self, item):
+        return getattr(self.f, item)
+    def read(self, n):
+        # print("reading total_bytes=%s" % n, flush=True)
+        if n >= (1 << 31):
+            buffer = bytearray(n)
+            idx = 0
+            while idx < n:
+                batch_size = min(n - idx, 1 << 31 - 1)
+                # print("reading bytes [%s,%s)..." % (idx, idx + batch_size), end="", flush=True)
+                buffer[idx:idx + batch_size] = self.f.read(batch_size)
+                # print("done.", flush=True)
+                idx += batch_size
+            return buffer
+        return self.f.read(n)
+    def write(self, buffer):
+        n = len(buffer)
+        print("writing total_bytes=%s..." % n, flush=True)
+        idx = 0
+        while idx < n:
+            batch_size = min(n - idx, 1 << 31 - 1)
+            print("writing bytes [%s, %s)... " % (idx, idx + batch_size), end="", flush=True)
+            self.f.write(buffer[idx:idx + batch_size])
+            print("done.", flush=True)
+            idx += batch_size
+
+
+
 def topickle(fl, sv_name):
     print(' ')
     print('Save to pickle |################################| 1/1')
     with open(sv_name+'.pkl', 'wb') as handle:
         pkl.dump(fl, handle, protocol=pkl.HIGHEST_PROTOCOL)
-
+        #joblib.dump(fl, handle)
 def frompickle(fl):
     with open(fl, 'rb') as handle:
         b = pkl.load(handle)
+        #b = joblib.load(handle)
     return b
 
 
@@ -83,6 +116,14 @@ def tojson(fl, sv_name):
     print('Save to json |################################| 1/1')
     with open(sv_name+'.json', 'w') as file:
         file.write(json.dumps(str(fl)))
+        #file.write(json.dumps(fl))
+def fromjson(fl):
+    print(' ')
+    print('Load to json |################################| 1/1')
+    with open(fl, 'r') as file:
+        data = file.read()
+        b = json.dumps(data)
+    return b
 
 def plot_surf(data, normal, c, save_name):
     #Plot surface
@@ -866,4 +907,4 @@ def togmxndx(box_res, fld, sv_name):
     bar.finish()
 
 def dict2pd(d, col=[]):
-    return pd.DataFrame.from_dict(d, orient='index', columns=col)
\ No newline at end of file
+    return pd.DataFrame.from_dict(d, orient='index', columns=col)

tooba_gmx.py

@@ -97,13 +97,18 @@ def rdf_peaks(TRR,TPR,IND,ST,EN,fld,arg1,arg2,dist_pk):
     p.communicate(cmd.encode('UTF-8'))
     p.send_signal('<Ctrl>-D')
     p.wait()
-
-    x,y=read_xvg(XVG=fld+'/tmp.xvg')
-    yhat = savgol_filter(y, 15, 4) # window size 15, polynomial order 4
-    peaks, _ = find_peaks(yhat, distance=dist_pk)
-
-    pathname = os.path.abspath(os.path.join(fld, 'tmp.xvg'))
-    os.remove(pathname)
+    try:
+      f = open(fld+'/tmp.xvg')
+      f.close()
+    # Do something with the file
+      x,y=read_xvg(XVG=fld+'/tmp.xvg')
+      yhat = savgol_filter(y, 15, 4) # window size 15, polynomial order 4
+      peaks, _ = find_peaks(yhat, distance=dist_pk)
+
+      pathname = os.path.abspath(os.path.join(fld, 'tmp.xvg'))
+      os.remove(pathname)
+    except IOError:
+      peaks=np.ndarray((0))
 
     return peaks
 
@@ -190,4 +195,4 @@ def order(TRR,TPR,IND,ST,EN,normal,fld,dist_pk=1):
     pathname = os.path.abspath(os.path.join(fld, 'tmp2.xvg'))
     os.remove(pathname)
 
-    return y
\ No newline at end of file
+    return y