plt_utils bug fixed

HISTORY.rst

@@ -158,4 +158,9 @@ History
 * default suffix in get_flist is *
 * logviewer.get_stack_of_files is only useful for reading data.
 * more tests are added.
-* moved multichannel_to_frame to utils
+* moved multichannel_to_frame to utils
+
+0.9.1 (2023-09-01)
+-----------------
+* bug removed from plt_utils numbers_as_images_4D.
+* bug removed from printprogress when number of steps is very low.

lognflow/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = 'Alireza Sadri'
 __email__ = '[email protected]'
-__version__ = '0.9.0'
+__version__ = '0.9.1'
 
 from .lognflow import lognflow
 from .logviewer import logviewer

lognflow/lognflow.py

@@ -1473,6 +1473,25 @@ def flush_all(self):
         for parameter_name in list(self._vars_dict):
             self.log_var_flush(parameter_name)
 
+    def save(self, parameter_name: str, 
+                   parameter_value,
+                   suffix = None,
+                   mat_field = None,
+                   time_tag: bool = None):
+        return self.log_single(parameter_name = parameter_name, 
+                               parameter_value = parameter_value,
+                               suffix = suffix,
+                               mat_field = mat_field,
+                               time_tag = time_tag)
+
+    def savez(self, parameter_name: str, 
+                    parameter_value,
+                    time_tag: bool = None):
+        return self.log_single(parameter_name = parameter_name, 
+                               parameter_value = parameter_value,
+                               suffix = 'npz',
+                               time_tag = time_tag)
+
     def __call__(self, *args, **kwargs):
         """calling the object
             In the case of the following code::
@@ -1492,23 +1511,4 @@ def __repr__(self):
         return f'{self.log_dir}'
 
     def __bool__(self):
-        return self.log_dir.is_dir()
-
-    def save(self, parameter_name: str, 
-                   parameter_value,
-                   suffix = None,
-                   mat_field = None,
-                   time_tag: bool = None):
-        return self.log_single(parameter_name = parameter_name, 
-                               parameter_value = parameter_value,
-                               suffix = suffix,
-                               mat_field = mat_field,
-                               time_tag = time_tag)
-
-    def savez(self, parameter_name: str, 
-                   parameter_value,
-                   time_tag: bool = None):
-        return self.log_single(parameter_name = parameter_name, 
-                               parameter_value = parameter_value,
-                               suffix = 'npz',
-                               time_tag = time_tag)
+        return self.log_dir.is_dir()

lognflow/logviewer.py

@@ -277,6 +277,10 @@ def get_stack_of_files(self,
         """
         if not flist:
             flist = self.get_flist(var_name, suffix)
+        else:
+            flist = list(flist)
+            assert pathlib.Path(flist[0]).is_file(), \
+                f'File not found: {flist[0]}. You can use logviewer get_flist'
 
         if flist:
             n_files = len(flist)

lognflow/plt_utils.py

@@ -1,3 +1,4 @@
+from .printprogress import printprogress
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 import numpy as np
 import matplotlib.pyplot as plt
@@ -41,10 +42,12 @@ def pltfig_to_numpy(fig):
     w,h = fig.canvas.get_width_height()
     buf = np.frombuffer(fig.canvas.tostring_argb(), dtype=np.ubyte)
     buf.shape = (w, h, 4)
-    buf = np.roll (buf, 3, axis = 2)
-    return buf
+    return buf.sum(2)
 
-def numbers_as_images_3D(dataset_shape: tuple, fontsize, verbose = False):
+def numbers_as_images_3D(data3D_shape: tuple[int, int, int],
+                         fontsize: int, 
+                         text_loc: tuple[int, int] = None,
+                         verbose: bool = True):
     """ Numbers3D
     This function generates a 4D dataset of images with shape
     (n_x, n_r, n_c) where in each image the value "x" is written as a text
@@ -61,8 +64,12 @@ def numbers_as_images_3D(dataset_shape: tuple, fontsize, verbose = False):
     output 3D array.
     
     """
-    n_x, n_r, n_c = dataset_shape
-    dataset = np.zeros(dataset_shape)    
+    n_x, n_r, n_c = data3D_shape
+
+    if text_loc is None:
+        text_loc = (n_r//2 - fontsize, n_c//2 - fontsize)
+
+    dataset = np.zeros(data3D_shape)    
     txt_width = int(np.log(n_x)/np.log(n_x)) + 1
     number_text_base = '{ind_x:0{width}}}'
     if(verbose):
@@ -71,22 +78,23 @@ def numbers_as_images_3D(dataset_shape: tuple, fontsize, verbose = False):
         mat = np.ones((n_r, n_c))
         number_text = number_text_base.format(ind_x = ind_x, 
                                               width = txt_width)
-        fig = plt.figure(figsize = (1, 1))
+        fig = plt.figure(figsize = (n_rr, n_cc), dpi = n_rc)
         ax = fig.add_subplot(111)
         ax.imshow(mat, cmap = 'gray', vmin = 0, vmax = 1)
-        ax.text(mat.shape[0]//2 - fontsize, mat.shape[1]//2 ,
+        ax.text(text_loc[0], text_loc[1],
                 number_text, fontsize = fontsize)
         ax.axis('off')
         buf = pltfig_to_numpy(fig)
         plt.close()
-        buf2 = buf[::buf.shape[0]//n_r, ::buf.shape[1]//n_c, :3].mean(2)
-        buf2 = buf2[:n_r, :n_c]
-        dataset[ind_x] = buf2.copy()
+        dataset[ind_x] = buf.copy()
         if(verbose):
             pBar()
     return dataset
 
-def numbers_as_images_4D(dataset_shape: tuple, fontsize, verbose = False):
+def numbers_as_images_4D(data4D_shape: tuple[int, int, int, int],
+                         fontsize: int, 
+                         text_loc: tuple[int, int] = None,
+                         verbose: bool = True):
     """ Numbers4D
     This function generates a 4D dataset of images with shape
     (n_x, n_y, n_r, n_c) where in each image the value "x, y" is written as a text
@@ -102,31 +110,38 @@ def numbers_as_images_4D(dataset_shape: tuple, fontsize, verbose = False):
     You can provide a logs_root, log_dir or simply select a directory to save the
     output 4D array.
     
+    :param text__loc:
+        text_loc should be a tuple of the location of bottom left corner of the
+        text in the image.
+    
     """
-    n_x, n_y, n_r, n_c = dataset_shape
+    n_x, n_y, n_r, n_c = data4D_shape
+
+    if text_loc is None:
+        text_loc = (n_r//2 - fontsize, n_c//2 - fontsize)
+
     dataset = np.zeros((n_x, n_y, n_r, n_c))    
     txt_width = int(np.log(np.maximum(n_x, n_y))
-                    /np.log(np.maximum(n_x, n_y))) + 1
+                    / np.log(np.maximum(n_x, n_y))) + 1
     number_text_base = '{ind_x:0{width}}, {ind_y:0{width}}'
     if(verbose):
         pBar = printprogress(n_x * n_y)
     for ind_x in range(n_x):
         for ind_y in range(n_y):
             mat = np.ones((n_r, n_c))
-            number_text = number_text_base.format(ind_x = ind_x, 
-                                                  ind_y = ind_y,
-                                                  width = txt_width)
-            fig = plt.figure(figsize = (1, 1))
+            number_text = number_text_base.format(
+                ind_x = ind_x, ind_y = ind_y, width = txt_width)
+            n_rc = np.minimum(n_r, n_c)
+            n_rr = n_r / n_rc
+            n_cc = n_c / n_rc
+            fig = plt.figure(figsize = (n_rr, n_cc), dpi = n_rc)
             ax = fig.add_subplot(111)
             ax.imshow(mat, cmap = 'gray', vmin = 0, vmax = 1)
-            ax.text(mat.shape[0]//2 - fontsize, mat.shape[1]//2 ,
-                    number_text, fontsize = fontsize)
+            ax.text(text_loc[0], text_loc[1], number_text, fontsize = fontsize)
             ax.axis('off')
             buf = pltfig_to_numpy(fig)
             plt.close()
-            buf2 = buf[::buf.shape[0]//n_r, ::buf.shape[1]//n_c, :3].mean(2)
-            buf2 = buf2[:n_r, :n_c]
-            dataset[ind_x, ind_y] = buf2.copy()
+            dataset[ind_x, ind_y] = buf.copy()
             if(verbose):
                 pBar()
     return dataset

lognflow/printprogress.py

@@ -47,7 +47,8 @@ def __init__(self,
         self.method = method
         self.in_print_function = print_function
         if(n_steps != int(n_steps)):
-            self._print_func('textProgBar takes integers no less than 2 ')
+            self._print_func(
+                r'printprogress takes integers no less than 2 as n_steps.')
             n_steps = int(n_steps)
         if(n_steps<2):
             n_steps = 2
@@ -75,6 +76,7 @@ def __init__(self,
         self._print_func(' \\')
 
         self._print_func(' ', end = '')
+        self.len_prog_text = 0
 
     def _print_func(self, text, end='\n'):
         if (self.in_print_function is not None):
@@ -93,7 +95,8 @@ def _calc_ETA(self):
 
     def __call__(self, ck=1):
         """ ticking the progress bar
-            just call the object and the progress bar moves one ahead when ready.
+            just call the object and the progress bar moves ck steps
+            ahead when ready.
             
             output
             ~~~~~~
@@ -104,12 +107,12 @@ def __call__(self, ck=1):
         if(self.FLAG_ended):
             if(not self.FLAG_warning):
                 self.FLAG_warning = True
-                self._print_func('-' * self.numTicks)
+                self._print_func('-' * (self.numTicks + 2))
         else:
             self.ck += ck
             if(self.ck <= self.n_steps):
                 remTimeS = self._calc_ETA() # useful when print_function is None
-                cProg = int(self.numTicks*self.ck/(self.n_steps-1)/3)    
+                cProg = int(self.numTicks*self.ck/(self.n_steps-1)/3)
                 #3: because 3 charachters are used
                 while((self.prog < cProg) & (not self.FLAG_ended)):
                     self.prog += 1
@@ -118,27 +121,33 @@ def __call__(self, ck=1):
                         progStr = "%02d" % int(ceil(remTimeS/86400))
                         self._print_func(progStr, end='')
                         self._print_func('d', end='')
+                        self.len_prog_text += 3
                     elif(remTimeS>5940): # less than 99h and more than 99m
                         progStr = "%02d" % int(ceil(remTimeS/3600))
                         self._print_func(progStr, end='')
                         self._print_func('h', end='')
+                        self.len_prog_text += 3
                     elif(remTimeS>99): # less than 99m and more than 99s
                         progStr = "%02d" % int(ceil(remTimeS/60))
                         self._print_func(progStr, end='')
                         self._print_func('m', end='')
+                        self.len_prog_text += 3
                     elif(remTimeS>=0): # less than 99s and more than 0
                         progStr = "%02d" % int(ceil(remTimeS))
                         self._print_func(progStr, end='')
                         self._print_func('s', end='')
+                        self.len_prog_text += 3
                     else:
-                        self.end()
-            if(self.ck >= self.n_steps):
-                self.end()
+                        self._end()
+            if((self.ck >= self.n_steps) | 
+               (self.len_prog_text >= self.numTicks)):
+                self._end()
         return remTimeS
-    def end(self):
+
+    def _end(self):
         if(not self.FLAG_ended):
             self._print_func('')
             self.FLAG_ended = True
 
     def __del__(self):
-        self.end()
+        self._end()

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.6
+current_version = 0.9.0
 commit = True
 tag = True
 

setup.py

@@ -6,7 +6,7 @@
 
 __author__ = 'Alireza Sadri'
 __email__ = '[email protected]'
-__version__ = '0.9.0'
+__version__ = '0.9.1'
 
 with open('README.rst') as readme_file:
     readme = readme_file.read()

tests/test_lognflow.py

@@ -329,7 +329,6 @@ def test_log_multichannel_by_subplots():
     logger.log_multichannel_by_subplots('images', images, (4, 5))
 
 if __name__ == '__main__':
-
     #-----IF RUN BY PYTHON------#
     temp_dir = select_directory()
     #---------------------------#

tests/test_printprogress.py

@@ -11,26 +11,11 @@
 import tempfile
 temp_dir = tempfile.gettempdir()
 
-@pytest.fixture
-def response():
-    """Sample pytest fixture.
-
-    See more at: http://doc.pytest.org/en/latest/fixture.html
-    """
-    # import requests
-    # return requests.get('https://github.com/audreyr/cookiecutter-pypackage')
-
-def test_content(response):
-    """Sample pytest test function with the pytest fixture as an argument."""
-    # from bs4 import BeautifulSoup
-    # assert 'GitHub' in BeautifulSoup(response.content).title.string
-
 def test_printprogress():
-    N = 3000000
-    pprog = printprogress(N)
-    for _ in range(N):
-        pprog()
-    # assert input('Did it show you a progress bar? (y for yes)')=='y'
+    for N in list([2, 4, 8, 10, 20, 200, 2000, 20000, 20000000]):
+        pprog = printprogress(N)
+        for _ in range(N):
+            pprog()
 
 def test_printprogress_with_logger():
     logger = lognflow(temp_dir)
@@ -62,8 +47,8 @@ def test_specific_timing():
     #-----IF RUN BY PYTHON------#
     temp_dir = select_directory()
     #---------------------------#
+    test_printprogress()
     test_printprogress_ETA()
     test_specific_timing()
     test_printprogress_with_logger()
-    test_printprogress()
-    exit()
+    exit()