Added print_tree, list_processes, last_process, and remove_process to core

Replaced colorm with cmap when plotting; colorm is still usable for now

current_functions.txt

@@ -13,7 +13,7 @@ be called using m_, l_, or e_apply.
     contour_closure            : removes features in an image below a certain size
     find_a_domains             : finds a-domains in amplitude image
     create_domain_wall_filter  : creates a filter around any binarised structure
-X    align_rows                 : aligns either rows or columns in image to have same average
+    align_rows                 : aligns either rows or columns in image to have same average
     threshold_ratio            : threshold function, where you pass ratios between max and min 
     directional_skeletonize    : skeletonizes figures into vertical or horizontal lines
     final_a_domains            : cleans a-domain images

hystorian/processing/core.py

@@ -229,6 +229,126 @@ def l_apply(filename, function, all_input_criteria, repeat=None, **kwargs):
         increment_proc = False
 
 
+def print_tree(filename, root=''):
+    '''
+    Prints the file structure of a .hdf5 file.
+
+    Parameters
+    ----------
+    filename : name of file to be examined
+    root : optional, allows showing only a subset of the tree (default : '')
+
+    Returns
+    -------
+    null
+    '''
+
+    def print_branches(name):
+        space = '    '
+        branch = '│   '
+        tee = '├── '
+        last = '└── '
+
+        shift = ''
+        curr_name_segments = (name.split('/'))
+        last_name_segments = []
+        for i in range((len(curr_name_segments))):
+            if i == 0:
+                if not root:
+                    last_name_segments.append(list(f.keys())[-1])
+                else:
+                    last_name_segments.append(list(f[root].keys())[-1])
+            else:
+                if not root:
+                    last_name_segments.append(list(f[name.rsplit('/', len(curr_name_segments) - i)[0]])[-1])
+                else:
+                    last_name_segments.append(list(f[root][name.rsplit('/', len(curr_name_segments) - i)[0]])[-1])
+        for i in range((len(curr_name_segments))):
+            curr_name = curr_name_segments[i]
+            last_name = last_name_segments[i]
+            if i != len(curr_name_segments) - 1:
+                if curr_name != last_name:
+                    shift += branch
+                else:
+                    shift += space
+            else:
+                if curr_name != last_name:
+                    shift += tee
+                else:
+                    shift += last
+        item_name = name.split("/")[-1]
+        print(shift + item_name)
+
+    with h5py.File(filename, "r") as f:
+        if root:
+            print(filename + '[' + root + ']')
+            f[root].visit(print_branches)
+        else:
+            print(filename)
+            f.visit(print_branches)
+
+
+def list_processes(filename, process=''):
+    '''
+    Returns a list of all processes in a named .hdf5 file.
+
+    Parameters
+    ----------
+    filename : name of file to be searched
+    process : optional, shortens the list of processes using regex (default : '')
+
+    Returns
+    -------
+    proclst : a list of all processes
+    '''
+
+    procs = np.array(pt.path_search(filename, 'process*' + process + '*')).ravel()
+    if len(procs) == 0:
+        return None
+    proclst = [p.split('/')[1].split('/')[0] for p in procs]
+    proclst = sorted(list(set(proclst)))
+    return proclst
+
+
+def last_process(filename, process=''):
+    '''
+    Returns a the filename of the last process as a string
+
+    Parameters
+    ----------
+    filename : name of file to be searched
+    process : optional, further qualifies the last process by a regex condition (default : '')
+
+    Returns
+    -------
+    final process filling the regex condition (if any)
+    '''
+    list_of_processes = list(list_processes(filename, process=''))
+    return (list_of_processes[-1])
+
+
+def remove_process(filename, process):
+    '''
+    Clears a named process from a named .hdf5 file. Note that the data is not de-allocated
+    in computer memory; use core.deallocate_hdf5_memory to regain memory.
+
+    Parameters
+    ----------
+    filename : name of file to be altered
+    process : string containing name of process to be removed
+
+    Returns
+    -------
+    null
+    '''
+    process_path = 'process/' + process
+    with h5py.File(filename, "a") as f:
+        if process_path in f.keys():
+            del f[process_path]
+            print(process_path + ' has been removed')
+        else:
+            print(process_path + ' not found')
+
 #   FUNCTION path_search
 # Uses regex expressions to search for all paths. Useful when writing complicated custom functions
 # that cannot use m_apply or l_apply

hystorian/processing/plot.py

@@ -17,7 +17,7 @@ def save_image(data,
                labelsize=16,
                full_range=False,
                std_range=3,
-               colorm='inferno',
+               cmap='inferno',
                colorbar=True,
                scalebar=False,
                physical_size=(0, 'unit'),
@@ -27,7 +27,8 @@ def save_image(data,
                image_name=None,
                saving_path='',
                source_path=None,
-               verbose=False):
+               verbose=False,
+               colorm=None):
 
     '''
     Wrapper around plt.imshow() and plt.savefig() to uniformize image saving
@@ -47,7 +48,7 @@ def save_image(data,
         (default: True)
     std_range: int or float, optional
         the number of standard deviation to use in case full_range is set to false. (default: 3)
-    colorm: str, optional
+    cmap: str, optional
         choose the colormap, see matplotlib for the list of available colormap (default: 'inferno')
     colorbar: bool, optional
         allows to remove the colorbar if set to false. (default: True)
@@ -76,6 +77,11 @@ def save_image(data,
     None
     '''
 
+    #Remove later
+    if colorm:
+        print('Use of \'colorm\' is depracated; use \'cmap\' instead')
+        cmap = colorm
+
     # Generate size of image frame
     if size is None:
         figsize = (np.array(np.shape(data)) / 100)[::-1]
@@ -107,7 +113,7 @@ def save_image(data,
         v_max = mean_val + std_range * std_val
 
     # Plot image
-    pos = plt.imshow(data, vmin=v_min, vmax=v_max, cmap=colorm)
+    pos = plt.imshow(data, vmin=v_min, vmax=v_max, cmap=cmap)
 
     # Generate colourbar
     if colorbar:

hystorian/processing/twodim.py

@@ -380,8 +380,7 @@ def generate_transform_xy_single(img, img_orig, offset_guess=[0,0],
     criteria = (term_flags, number_of_iterations, termination_eps)
     warp_matrix[0, 2] = offset_guess[0]
     warp_matrix[1, 2] = offset_guess[1]
-    (cc, tform21) = cv2.findTransformECC(img_orig, img, warp_matrix, warp_mode,
-                                         criteria, None, 1)
+    (cc, tform21) = cv2.findTransformECC(img_orig, img, warp_matrix, warp_mode, criteria)
     return tform21