Merge branch '9984c47'

README.rst

@@ -32,8 +32,7 @@ You can get the most updated version by cloning the source code from github and
 
 To do this:
 
-1. use the ``Code`` button at top of page, or clone from command-lineç
-``git clone https://github.com/vincenzooo/pyXSurf.git``. 
+1. use the ``Code`` button at top of page, or clone from command-line: ``git clone https://github.com/vincenzooo/pyXSurf.git``. 
 
 2. move to the folder with the code and call from command line ``pip install .`` (equivalent to ``python setup.py install``). 
 This will perform a "regular" installation  (meaning that the code is copied to ``site-packages`` folders, which holds all installed Python libraries, and made accessible to your system).
@@ -44,7 +43,7 @@ If instead you plan to modify pyXsurf code, or want a non-permanente installatio
 Uninstalling
 ------------
 
-Code can be uninstalled calling ``pip uninstall pyXsurf`` from a command prompt, or from source code folder calling directly the setup file ``python setup.py develop  -u`` (if you installed as developer, deinstallation is expected to work only with most recent pip versions, at least >=19.1.1, otherwise it should be enough to delete the folder).
+Code can be uninstalled calling ``pip uninstall pyXsurf`` from a command prompt. N.B.: previous version can also be uninstalled from source code folder calling directly the setup file ``python setup.py develop  -u``, this is no more advised (if you installed as developer, deinstallation is expected to work only with most recent pip versions, at least >=19.1.1, otherwise it should be enough to delete the folder).
 
 How to use
 ==========
@@ -54,7 +53,9 @@ works without errors, you can now import and use the different modules (see desc
 
 .. code:: python
 
-    from pySurf.data2D import data2D
+    from pySurf.data2D_class import Data2D
+
+or try the library in a Jupyter notebook, you can start from the example `pySurf_demo.ipynb`, in the install folder.
 
 In addition to the `official documentation <https://pyxsurf.readthedocs.io>`_ , you can find examples and data in a ``test`` subfolder of each
 module and at the end of module files. Functions are usually documented with docstrings (but these might be in the wrong place, please be patient and look well in the code). 

source/dataIO/arrays.py

@@ -242,11 +242,25 @@ def vectorize(arg, n, force_if_n=False):
     
     """
 
+# <<<<<<< HEAD
     if (real_len(arg) != n) or force_if_n:        
         try:
             arg=[arg.deepcopy() for _ in range(n)]
         except AttributeError:  #fails e.g. if tuple which don't have copy method
             arg=[arg for _ in range(n)]  
+# =======
+#     #FIXME: this is still not a reliable mechanism, see extended tests below.
+#     # in other cases used len(np.shape), maybe works better, e.g.:
+#     # if len(np.shape(reader)) == 0: #vectorize #np.size(reader) == 1:
+#     # reader=[reader]*len(rfiles)
+
+#     if args:
+#         for a in args:
+#             if (np.size(a) == 1):
+#                 args=[[] for i in range(n)]    
+#             elif (len(a) != n):
+#                 args=[args for i in range(n)]  
+# >>>>>>> 9984c47
     else:
         if (n == 1) and len(np.shape(arg)) == 0:
             arg = [arg]    
@@ -272,12 +286,50 @@ def test_vectorize():
 
     assert vectorize([1,2,3], 2) == [[1,2,3],[1,2,3]]
     assert vectorize([], 3) == [[],[],[]]
+
+    # <<<<<<< HEAD
     assert vectorize([1,2,3], 3, True) == [[1,2,3],[1,2,3],[1,2,3]]
 
     assert vectorize([[1,2],[3,4]],2) == [[1,2],[3,4]]
     assert vectorize([[1,2],[3,4]],2,True) == [[[1,2],[3,4]],[[1,2],[3,4]]]
 
     print('All tests passed.')
+    # =======
+    assert vectorize([1,2,3], 3) == [[1,2,3],[1,2,3],[1,2,3]]
+
+    #extended test
+    a = []
+    b = 5
+    c = [3]
+
+    print("(a,3) --> ",vectorize(a,3))
+    print("(a,1) --> ",vectorize(a,1))
+    print("(b,3) --> ",vectorize(b,3))
+    print("(b,1) --> ",vectorize(b,1))
+    print("(c,3) --> ",vectorize(c,3))
+    print("(c,1) --> ",vectorize(c,1))
+
+    b = 'cane'
+    c = ['cane']
+
+    print("(b,3) --> ",vectorize(b,3))
+    print("(b,1) --> ",vectorize(b,1))
+    print("(c,3) --> ",vectorize(c,3))
+    print("(c,1) --> ",vectorize(c,1))
+    # >>>>>>> 9984c47
+
+
+def inspect_vector(obj):
+    """Print a set of dimensional information about the object.
+    
+    The returned information should be useful to discriminate between different lengths, dimensions and rank.
+    
+    """
+
+    print("len: ",len(obj))
+    print("np.size: ",np.size(obj))
+    print("np.shape: ",np.shape(obj))
+    print("len of shape: ",len(np.shape(obj)))
 
 def make_raster(*vectors, as_axis = False, extend = True):
     """Create a raster grid on the base of a list of vectors.

source/dataIO/files.py

@@ -5,6 +5,31 @@
 import warnings
 warnings.filterwarnings("error", category=np.VisibleDeprecationWarning) 
 
+def files_with_ext(base_folder, folder_glob_pattern= "", file_extension=".*"):
+    """
+    Find files with a given extension within folders matching a glob pattern.
+
+    :param base_folder: The base directory to start the search from.
+    :param folder_glob_pattern: The glob pattern to match folders.
+    :param file_extension: The extension of the files to find. Pass empty string for folders or files with no extension.
+    :return: A list of paths to files matching the given extension in folders matching the glob pattern.
+    """
+    from pathlib import Path
+
+    # Define the base path to start searching from
+    base_path = Path(base_folder)
+
+    # Initialize a list to hold the matched file paths
+    matched_files = []
+
+    # Find all folders matching the glob pattern
+    for folder in base_path.glob(folder_glob_pattern):
+        if folder.is_dir():  # Ensure the matched path is a directory
+            # Use rglob to find all files with the given extension in the current folder and its subfolders
+            matched_files.extend(str(f) for f in folder.rglob(f'*{file_extension}'))
+
+    return matched_files
+
 def read_blocks(filename,delimiter = '\n\n', comment = None,*args,**kwargs):
     """Read a file containing blocks of numerical data separated by a white line.
     
@@ -37,20 +62,19 @@ def read_blocks(filename,delimiter = '\n\n', comment = None,*args,**kwargs):
 
     return pList
 
-
-def print_results(a, title):
-    '''pass result and descriptive title for a test.'''
-
-    print('\n====== ',title, ' ======\n')
-    print('%i blocks read'%len(a))
-    print('block shapes: ',[aa.shape for aa in a])
-    print('block contents: ')
-    for i,aa in enumerate(a):
-        print('block #%i:\n'%(i+1),'[%s\n..\n..\n%s]\n'%(','.join(map(str,aa[:3])),','.join(map(str,aa[-2:]))))
-    return a
-
 def test_read_blocks(filename=None):
 
+    def print_results(a, title):
+        '''pass result and descriptive title for a test.'''
+
+        print('\n====== ',title, ' ======\n')
+        print('%i blocks read'%len(a))
+        print('block shapes: ',[aa.shape for aa in a])
+        print('block contents: ')
+        for i,aa in enumerate(a):
+            print('block #%i:\n'%(i+1),'[%s\n..\n..\n%s]\n'%(','.join(map(str,aa[:3])),','.join(map(str,aa[-2:]))))
+        return a
+
     #infolder = r'C:\Users\kovor\Documents\python\pyXTel\source\pyProfile\test\input_data\'
 
     infolder = r'C:\Users\kovor\Documents\python\pyXTel\source\dataIO\test\test_data\blocks'

source/dataIO/roi.py

@@ -1,4 +1,4 @@
 
 
-# 2020/10/25 functions were here, not sure why, moved in pySurf.roi
+# 2020/10/25 functions were here, not sure why, moved to pySurf.roi
 

source/plotting/plot_positions.py

@@ -20,18 +20,29 @@ def plot_poly(v,ls='',ms=''):
     #plot lines
     return plt.plot(mh[:,0],mh[:,1],ls)[0]
 '''
-
+
+import numpy as np
+
 def plot_poly(v,*args,**kwargs):
     """plot a polygon defined by a list of vertices `v` as coordinate couples.
-    Just a thin wrapper around `plt.plot`, it just accepts points in transpose form and adds a copy of first point at the."""
+    
+    Just a thin wrapper around `plt.plot`, it just accepts points in transpose form and adds a copy of first point at the end.
+   
+    Accept all matplotlib keywords, e.g.;
+        hatch = '/',
+        facecolor = 'none'
+        edgecolor = 'black'
+        
+    for line-filled black shape. The default is a filled shape with matplotlib next color (TODO: change it to empty shape with matplotlib color for lines). The three parameters in the example probabily need all to be set for hatched shapes. 
+    """
 
     v=np.array(v)
     # duplicate first point at the end: 
     v=np.vstack([v,v[0,:]]) 
     # plt.plot return a list of one element
 
-    #plot lines
-    return plt.plot(*v.T,*args,**kwargs)
+    # plot lines
+    return plt.fill(*v.T,*args,**kwargs) # plt.plot(*v.T,*args,**kwargs)
 
 def plot_rect(c1,c2,*args,**kwargs):
     """plot a polygon defined by a 2 element list with coordinates of opposite corners.

source/pyProfile/profile_class.py

@@ -250,9 +250,10 @@ def __init__(self,x=None,y=None,file=None,reader=None,
             x=None
         else:
             if y is not None:
-                y=np.array(y) #onvert to array if not
-
-        #pdb.set_trace()
+                y=np.array(y) #convert to array if not
+                x=np.array(x)
+        # import pdb
+        # pdb.set_trace()
         self.file=file #initialized to None if not provided
         if file is not None:
             assert y is None
@@ -306,9 +307,10 @@ def __init__(self,x=None,y=None,file=None,reader=None,
                     x=np.arange(np.size(y))  
 
     #if data is not None:
-        self.x, self.y = x, y
+        # self.x, self.y = np.array(x), np.array(y)
 
-        self.x,self.y=register_profile(self.x,self.y,scale=scale,*args,**kwargs) # se load_profile calls register, this
+        breakpoint()
+        self.x,self.y=register_profile(np.array(x), np.array(y),scale=scale,*args,**kwargs) # se load_profile calls register, this
         #goes indented.
 
         if np.size(units) == 1:
@@ -567,7 +569,7 @@ def __rtruediv__(self,other):
 
         res = self.copy()
         if np.size(other) == 1:
-            if isinstance(other,self):  # scalar
+            if isinstance(other,self.__class__):  # scalar
                 sel = (self.y != 0) 
                 res = self.copy()
                 res.y[sel] = other*(1./self.y[sel])
@@ -637,7 +639,7 @@ def merge(self,other,*args,**kwargs):
         if isinstance(other,self.__class__):
             #res = merge_profiles([[self.x,self.y],[other.x,other.y]],*args,**kwargs)
             res = merge_profile(self.x,self.y,other.x,other.y,*args,**kwargs)
-            res = Profile(*res,units=self.units,name=self.name + " // " + other.name)
+            res = self.__class__(*res,units=self.units,name=self.name + " // " + other.name)
         else:
             raise ValueError("Unrecognized type in merge")
         return res
@@ -1040,6 +1042,17 @@ def __init__(self, *args, **kwargs):
     """ N.B.: TODO: could use linecollections for plotting https://matplotlib.org/stable/api/collections_api.html#matplotlib.collections.LineCollection
     """
 
+    def merge(self, mode='raw',*args,**kwargs):
+        res = self[0]
+        for p in self[1:]:
+            res = res.merge(p,*args,**kwargs)
+        return res
+
+    def save(self,file, type= 'vstack', *args,**kwargs):
+        """save stacked or on separate files"""
+        pp = self.merge()
+        pp.save(file, *args,**kwargs)
+
 def test_load_plist(rfiles = None):
 
     if rfiles is None:

source/pySurf/data2D.py

@@ -240,7 +240,7 @@ def _validate_degree(degree, axis):
             raise ValueError("Degree must be scalar when leveling by line (axis != None): received {}".format(degree))
         return degree
 
-    def _level_by_line(data, degree, *args, **kwargs):
+    def _level_by_line(data, y, degree, *args, **kwargs):
         leg = fitlegendre(y, data, degree, *args, **kwargs)
         return leg
 
@@ -258,9 +258,9 @@ def _level_plane(data, degree, *args, **kwargs):
     degree = _validate_degree(degree, axis)
 
     if axis == 0:
-        leg = _level_by_line(data, degree, *args, **kwargs)
+        leg = _level_by_line(data, y, degree, *args, **kwargs)
     elif axis == 1:
-        leg = _level_by_line(data.T, degree, *args, **kwargs).T
+        leg = _level_by_line(data.T, x, degree, *args, **kwargs).T
     elif axis is None:
         leg = _level_plane(data, degree, *args, **kwargs)
     else:

source/pySurf/data2D_class.py

@@ -430,8 +430,10 @@ def rotate(self, angle, *args, **kwargs):
         """call data2D.rotate_data, which rotate array of an arbitrary angle in degrees in direction
         (from first to second axis)."""
         res = self.copy()
+        # FIXME: rotation doesn't work without conversion to points.
+        usepoints =  kwargs.pop("usepoints",True)
         res.data, res.x, res.y = rotate_data(
-            self.data, self.x, self.y, angle, *args, **kwargs
+            self.data, self.x, self.y, angle, usepoints=usepoints, *args, **kwargs
         )
         return res
 
@@ -530,7 +532,7 @@ def apply_to_data(self, func, *args, **kwargs):
     def crop(self, *args, **kwargs):
         """crop data making use of function data2D.crop_data, where data,x,y are taken from a"""
         res = self.copy()
-        res.data, res.x, res.y = crop_data(self.data, self.x, self.y, *args, **kwargs)
+        res.data, res.x, res.y = crop_data(res.data, res.x, res.y, *args, **kwargs)
         return res
 
     crop = update_docstring(crop, crop_data)
@@ -561,6 +563,32 @@ def resample(self, other, *args, **kwargs):
 
     resample = update_docstring(resample, resample_data)
 
+    def divide_and_crop(self, n, m):
+        """Divide data in n x m equal size data. Data, returned as Dlsit, are ordered as coordinates."""
+
+        xmin,xmax = span(self.x)
+        ymin,ymax = span(self.y)
+
+        # Width and height of each sub-rectangle
+        x_step = (xmax - xmin) / n
+        y_step = (ymax - ymin) / m
+
+        dl = []
+        # Nested loops to iterate over each sub-rectangle
+        for j in range(m):
+            for i in range(n):
+                # Calculating the bounds for this sub-rectangle
+                x_start = xmin + i * x_step
+                x_end = xmin + (i + 1) * x_step
+                y_start = ymax - (j + 1) * y_step
+                y_end = ymax - j * y_step
+                dd = self.crop((x_start, x_end), (y_start, y_end))
+                dd.name = fn_add_subfix(dd.name, ' (%i,%i)'%(i,j))
+                # Call the crop function with the calculated bounds
+                dl.append(dd)
+
+        return Dlist(dl)
+
     def add_markers(self, *args, **kwargs):
         #f = plt.figure()
         self.plot()
@@ -805,7 +833,7 @@ def plot(self,linear = False,*args, **kwargs):
 
 
     def avgpsd(self, *args, **kwargs):
-        """avg, returns f and p. Can use data2D.projection keywords `span` and `expand` to return PSD ranges."""
+        """avg, returns a PSD (linear) object. Can use data2D.projection keywords `span` and `expand` to return PSD ranges."""
 
         #return Profile(self.y, projection(self.data, axis=1, *args, **kwargs), units = [self.units[1], self.units[2]]) 
         res = super().projection(axis = 1, *args, **kwargs)

source/pySurf/points.py

@@ -285,9 +285,11 @@ def points_find_hull(pts):
     plt.plot(hull[:,0], hull[:,1], 'r--', lw=2)."""
 
     from scipy.spatial import ConvexHull
-    if pts.shape[1] == 2:
+
+    pts = np.array(pts)
+    if np.shape(pts)[1] == 2:
         xypts = pts
-    elif pts.shape[1] == 3:
+    elif np.shape(pts)[1] == 3:
         xypts=pts[~np.isnan(pts[:,2]),:2]
     else:
         raise ValueError("wrong shape for points in points_find_hull")
@@ -389,7 +391,7 @@ def matrix_to_points(data,xgrid,ygrid,transpose=False):
     return np.vstack([x.flatten(),y.flatten(),data.T.flatten()]).T
 
 
-def get_points(filename,x=None,y=None,xrange=None,yrange=None,matrix=False,addaxis=False,scale=None,center=None,skip_header=None,delimiter=','):
+def get_points(filename,x=None,y=None,xrange=None,yrange=None,matrix=False,addaxis=False,scale=None,center=None,skip_header=None,delimiter=',',*args,**kwargs):
     """
     Return a set of xyz points (N,3) from generic csv files in xyz or matrix format.
 
@@ -448,7 +450,7 @@ def get_points(filename,x=None,y=None,xrange=None,yrange=None,matrix=False,addax
     else:
         skip=skip_header
 
-    mdata=np.genfromtxt(filename,skip_header=skip,delimiter=delimiter)
+    mdata=np.genfromtxt(filename,skip_header=skip,delimiter=delimiter,*args,**kwargs)
     if (matrix):
         if addaxis == True: addaxis = 'xy'