From e1a32f8f9ef5b7b06906bae1238847da7b8ef51b Mon Sep 17 00:00:00 2001 From: erdogant Date: Sun, 19 Nov 2023 21:17:06 +0100 Subject: [PATCH] 2.6.1 --- docs/pages/doctrees/Mask.doctree | Bin 9157 -> 9207 bytes docs/pages/doctrees/Plots.doctree | Bin 22555 -> 22499 bytes docs/pages/doctrees/Pre-processing.doctree | Bin 28297 -> 28387 bytes docs/pages/doctrees/Topology.doctree | Bin 48707 -> 48797 bytes docs/pages/doctrees/Use-cases.doctree | Bin 36603 -> 36795 bytes docs/pages/doctrees/environment.pickle | Bin 941809 -> 942175 bytes docs/pages/html/Mask.html | 2 +- docs/pages/html/Plots.html | 4 ++-- docs/pages/html/Pre-processing.html | 4 ++-- docs/pages/html/Topology.html | 4 ++-- docs/pages/html/Use-cases.html | 8 ++++---- docs/pages/html/_sources/Mask.rst.txt | 2 +- docs/pages/html/_sources/Plots.rst.txt | 4 ++-- .../html/_sources/Pre-processing.rst.txt | 4 ++-- docs/pages/html/_sources/Topology.rst.txt | 4 ++-- docs/pages/html/_sources/Use-cases.rst.txt | 8 ++++---- 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z1s79IW@T*#AB}Hrh>phSK=OOaG$P-+oG@)Vi;FnpGI?fCeet*^;~eBqV*#K}XAa>a z9GZ?N!GFVd)A7W42_j~o`T-`+VDa$Qbo@%wH3M&HpU+?eJd$1IzlSeoupkd(U0fzR zO1Qvj2${)j!cQ=0CY~&Rg|RbPQfL1;d~5oiNAV`1-6TB7yq(bdB=(W`gv16CkCNyj z(N5wq5)YC1jl@$VJ|b}!iE0v8NmwbVH;G%wypP0f=V)g>Pw-U|CUVapR7qk7i3=p& zCb5>p6C`Ac`sB*3+c#OnPBuTwo-dimensional dataXdetect and Xranked has the same shape as the input data. The elements with value > 0 depict a region of interest.

Plot the image with the detected peaks:

# Import library
-fp.plot()
+fp.plot(figure_order='horizontal')
diff --git a/docs/pages/html/Plots.html b/docs/pages/html/Plots.html index a0ecf34..a27199e 100644 --- a/docs/pages/html/Plots.html +++ b/docs/pages/html/Plots.html @@ -212,7 +212,7 @@

Pre-processing plot
# Import library
 from findpeaks import findpeaks
 # Initialize
-fp = findpeaks(method='topology', scale=True, denoise='fastnl', window=3, togray=True, imsize=(50,150))
+fp = findpeaks(method='topology', whitelist=['peak'])
 # Import example
 X = fp.import_example("2dpeaks")
 # Detect peaks
@@ -240,7 +240,7 @@ 
Plot<
 
 
 
# Plot
-fp.plot()
+fp.plot(figure_order='horizontal')
 

 

 
diff --git a/docs/pages/html/Pre-processing.html b/docs/pages/html/Pre-processing.html
index deb2f64..7905a2b 100644
--- a/docs/pages/html/Pre-processing.html
+++ b/docs/pages/html/Pre-processing.html
@@ -278,13 +278,13 @@ 
Preprocessing
# Import library
 from findpeaks import findpeaks
 # Init
-fp = findpeaks(method="topology", imsize=(50,100), scale=True, togray=True, denoise=None)
+fp = findpeaks(method="topology", whitelist=['peak'], imsize=(50,100), scale=True, togray=True, denoise=None)
 # Small dataset
 X = fp.import_example("2dpeaks")
 
 # Interpolate the data using linear by factor 10
 results = fp.fit(X)
-fp.plot()
+fp.plot(figure_order='horizontal')
 # fp.plot_persistence()
 

 
diff --git a/docs/pages/html/Topology.html b/docs/pages/html/Topology.html
index 0ec460d..b482962 100644
--- a/docs/pages/html/Topology.html
+++ b/docs/pages/html/Topology.html
@@ -380,7 +380,7 @@ 
Two-dimensional
# Import library
 from findpeaks import findpeaks
 # Initialize
-fp = findpeaks(method='topology')
+fp = findpeaks(method='topology', whitelist=['peak'])
 # Example 2d image
 X = fp.import_example('2dpeaks')
 # Fit topology method on the 1d-vector
@@ -394,7 +394,7 @@ 
Two-dimensional
# Import library
-fp.plot()
+fp.plot(figure_order='horizontal')
 

 

 

diff --git a/docs/pages/html/Use-cases.html b/docs/pages/html/Use-cases.html
index fb034e5..e3624f3 100644
--- a/docs/pages/html/Use-cases.html
+++ b/docs/pages/html/Use-cases.html
@@ -247,7 +247,7 @@ 
SAR# Fit
 fp.fit(img)
 # Thousands of peaks are detected at this point.
-fp.plot()
+fp.plot(figure_order='horizontal')
 fp.plot_mesh()
 
 
@@ -266,7 +266,7 @@ 
SAR# Import image example
 img = fp.import_example('2dpeaks_image')
 # Initializatie
-fp = findpeaks(scale=True, denoise='fastnl', params={'window': 31}, togray=True, imsize=(300,300))
+fp = findpeaks(method='topology', limit=160, scale=True, togray=True, imsize=(150, 150), denoise='lee_sigma', params={'window': 17})
 # Fit
 fp.fit(img)
 
@@ -287,7 +287,7 @@ 
SAR
 
In the next step, we can examine the detected peaks (see below). But these peaks are barely visible on the plot. Nevertheless, we seem to removed many peaks compared to the not-preprocessed image.

 
# Plot
-fp.plot()
+fp.plot(figure_order='horizontal')
 

 

 

@@ -372,7 +372,7 @@ 
SAR
 
Denoising
from findpeaks import findpeaks
-fp = findpeaks()
+fp = findpeaks(limit=160)
 img = fp.import_example('2dpeaks_image')
 import findpeaks
 
diff --git a/docs/pages/html/_sources/Mask.rst.txt b/docs/pages/html/_sources/Mask.rst.txt
index 9d51bd1..e9ef7f1 100644
--- a/docs/pages/html/_sources/Mask.rst.txt
+++ b/docs/pages/html/_sources/Mask.rst.txt
@@ -42,7 +42,7 @@ Plot the image with the detected peaks:
 .. code:: python
 
     # Import library
-    fp.plot()
+    fp.plot(figure_order='horizontal')
 
 .. _Figure_6:
 
diff --git a/docs/pages/html/_sources/Plots.rst.txt b/docs/pages/html/_sources/Plots.rst.txt
index 1f9cde8..ed2e7bd 100644
--- a/docs/pages/html/_sources/Plots.rst.txt
+++ b/docs/pages/html/_sources/Plots.rst.txt
@@ -65,7 +65,7 @@ Depending on the number of user defined pre-processing steps, the plot will add
     # Import library
     from findpeaks import findpeaks
     # Initialize
-    fp = findpeaks(method='topology', scale=True, denoise='fastnl', window=3, togray=True, imsize=(50,150))
+    fp = findpeaks(method='topology', whitelist=['peak'])
     # Import example
     X = fp.import_example("2dpeaks")
     # Detect peaks
@@ -95,7 +95,7 @@ The **plot** function :func:`findpeaks.findpeaks.findpeaks.plot` plots the 3 maj
 .. code:: python
 
     # Plot
-    fp.plot()
+    fp.plot(figure_order='horizontal')
 
 
 .. |figP1| image:: ../figs/plot_example1.png
diff --git a/docs/pages/html/_sources/Pre-processing.rst.txt b/docs/pages/html/_sources/Pre-processing.rst.txt
index 6084ff4..24b7520 100644
--- a/docs/pages/html/_sources/Pre-processing.rst.txt
+++ b/docs/pages/html/_sources/Pre-processing.rst.txt
@@ -134,13 +134,13 @@ Each of these steps can be controlled by setting the input parameters.
     # Import library
     from findpeaks import findpeaks
     # Init
-    fp = findpeaks(method="topology", imsize=(50,100), scale=True, togray=True, denoise=None)
+    fp = findpeaks(method="topology", whitelist=['peak'], imsize=(50,100), scale=True, togray=True, denoise=None)
     # Small dataset
     X = fp.import_example("2dpeaks")
 
     # Interpolate the data using linear by factor 10
     results = fp.fit(X)
-    fp.plot()
+    fp.plot(figure_order='horizontal')
     # fp.plot_persistence()
 
 
diff --git a/docs/pages/html/_sources/Topology.rst.txt b/docs/pages/html/_sources/Topology.rst.txt
index a88ac4f..173055b 100644
--- a/docs/pages/html/_sources/Topology.rst.txt
+++ b/docs/pages/html/_sources/Topology.rst.txt
@@ -259,7 +259,7 @@ The docstring provide the information regarding the input/output parameters: :fu
     # Import library
     from findpeaks import findpeaks
     # Initialize
-    fp = findpeaks(method='topology')
+    fp = findpeaks(method='topology', whitelist=['peak'])
     # Example 2d image
     X = fp.import_example('2dpeaks')
     # Fit topology method on the 1d-vector
@@ -276,7 +276,7 @@ Plot the image with the detected peaks:
 .. code:: python
 
     # Import library
-    fp.plot()
+    fp.plot(figure_order='horizontal')
 
 .. _Figure_5:
 
diff --git a/docs/pages/html/_sources/Use-cases.rst.txt b/docs/pages/html/_sources/Use-cases.rst.txt
index 2496694..247fa2e 100644
--- a/docs/pages/html/_sources/Use-cases.rst.txt
+++ b/docs/pages/html/_sources/Use-cases.rst.txt
@@ -108,7 +108,7 @@ Let's load a SAR image, apply denoising techniques and then detect peaks.
     # Fit
     fp.fit(img)
     # Thousands of peaks are detected at this point.
-    fp.plot()
+    fp.plot(figure_order='horizontal')
     fp.plot_mesh()
 
 
@@ -134,7 +134,7 @@ From this point on, we will *pre-process* the image and apply the *topology* met
     # Import image example
     img = fp.import_example('2dpeaks_image')
     # Initializatie
-    fp = findpeaks(scale=True, denoise='fastnl', params={'window': 31}, togray=True, imsize=(300,300))
+    fp = findpeaks(method='topology', limit=160, scale=True, togray=True, imsize=(150, 150), denoise='lee_sigma', params={'window': 17})
     # Fit
     fp.fit(img)
     
@@ -163,7 +163,7 @@ In the next step, we can examine the detected peaks (see below). But these peaks
 .. code:: python
 
     # Plot
-    fp.plot()
+    fp.plot(figure_order='horizontal')
 
 
 .. |figU1| image:: ../figs/sonar_plot.png
@@ -267,7 +267,7 @@ Denoising
 .. code:: python
 
 	from findpeaks import findpeaks
-	fp = findpeaks()
+	fp = findpeaks(limit=160)
 	img = fp.import_example('2dpeaks_image')
 	import findpeaks
 
diff --git a/docs/pages/html/searchindex.js b/docs/pages/html/searchindex.js
index affde75..909200b 100644
--- a/docs/pages/html/searchindex.js
+++ b/docs/pages/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["Abstract", "Caerus", "Coding quality", "Denoise", "Documentation", "Examples", "Installation", "Mask", "Peakdetect", "Performance", "Plots", "Pre-processing", "Topology", "Use-cases", "findpeaks.findpeaks", "index", "sponsor"], "filenames": ["Abstract.rst", "Caerus.rst", "Coding quality.rst", "Denoise.rst", "Documentation.rst", "Examples.rst", "Installation.rst", "Mask.rst", "Peakdetect.rst", "Performance.rst", "Plots.rst", "Pre-processing.rst", "Topology.rst", "Use-cases.rst", "findpeaks.findpeaks.rst", "index.rst", "sponsor.rst"], "titles": ["Abstract", "Caerus", "Coding quality", "Denoise", "Sponsor", "Quick Examples", "Quickstart", "Mask", "Peakdetect", "Performance", "One-dimensional plots", "Interpolate/impute", "Topology", "Stock Markets", "Description", "findpeaks\u2019s documentation!", "<no title>"], "terms": {"background": [0, 7], "The": [0, 1, 2, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14], "detect": [0, 3, 4, 6, 7, 10, 11, 12, 14, 15], "peak": [0, 3, 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\ No newline at end of file
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"calculate_all_mi() (in module findpeaks.filters.frost)": [[14, "findpeaks.filters.frost.calculate_all_Mi"]], "calculate_local_weight_matrix() (in module findpeaks.filters.frost)": [[14, "findpeaks.filters.frost.calculate_local_weight_matrix"]], "compute_coef_var() (in module findpeaks.filters.frost)": [[14, "findpeaks.filters.frost.compute_coef_var"]], "denoise() (in module findpeaks.stats)": [[14, "findpeaks.stats.denoise"]], "disable_tqdm() (in module findpeaks.stats)": [[14, "findpeaks.stats.disable_tqdm"]], "findpeaks (class in findpeaks.findpeaks)": [[14, "findpeaks.findpeaks.findpeaks"]], "findpeaks.filters.frost": [[14, "module-findpeaks.filters.frost"]], "findpeaks.filters.kuan": [[14, "module-findpeaks.filters.kuan"]], "findpeaks.filters.lee": [[14, "module-findpeaks.filters.lee"]], "findpeaks.filters.lee_enhanced": [[14, "module-findpeaks.filters.lee_enhanced"]], "findpeaks.filters.mean": [[14, "module-findpeaks.filters.mean"]], "findpeaks.filters.median": [[14, 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"module-findpeaks.findpeaks"], [14, "module-findpeaks.interpolate"], [14, "module-findpeaks.stats"]], "normalize() (in module findpeaks.stats)": [[14, "findpeaks.stats.normalize"]], "peaks1d() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.peaks1d"]], "peaks2d() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.peaks2d"]], "plot() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot"]], "plot() (in module findpeaks.interpolate)": [[14, "findpeaks.interpolate.plot"]], "plot1d() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot1d"]], "plot2d() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot2d"]], "plot_mask() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot_mask"]], "plot_mesh() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot_mesh"]], "plot_persistence() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot_persistence"]], "plot_preprocessing() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.plot_preprocessing"]], "preprocessing() (findpeaks.findpeaks.findpeaks method)": [[14, "findpeaks.findpeaks.findpeaks.preprocessing"]], "resize() (in module findpeaks.stats)": [[14, "findpeaks.stats.resize"]], "reverse_values() (in module findpeaks.stats)": [[14, "findpeaks.stats.reverse_values"]], "scale() (in module findpeaks.stats)": [[14, "findpeaks.stats.scale"]], "togray() (in module findpeaks.stats)": [[14, "findpeaks.stats.togray"]], "topology() (in module findpeaks.stats)": [[14, "findpeaks.stats.topology"]], "topology2d() (in module findpeaks.stats)": [[14, "findpeaks.stats.topology2d"]], "weighting() (in module findpeaks.filters.kuan)": [[14, "findpeaks.filters.kuan.weighting"]], "weighting() (in module findpeaks.filters.lee_enhanced)": [[14, "findpeaks.filters.lee_enhanced.weighting"]]}})
\ No newline at end of file
diff --git a/findpeaks/__init__.py b/findpeaks/__init__.py
index cc6dca9..3e1265a 100644
--- a/findpeaks/__init__.py
+++ b/findpeaks/__init__.py
@@ -23,7 +23,7 @@
 
 __author__ = 'Erdogan Tasksen'
 __email__ = 'erdogant@gmail.com'
-__version__ = '2.6.0'
+__version__ = '2.6.1'
 
 # module level doc-string
 __doc__ = """
diff --git a/findpeaks/examples.py b/findpeaks/examples.py
index b8c7946..94a4b3e 100644
--- a/findpeaks/examples.py
+++ b/findpeaks/examples.py
@@ -92,6 +92,7 @@
                imsize=(150, 150),
                denoise='lee_sigma',
                params={'window': 17},
+               limit=160,
                )
 
 # Import example image
@@ -102,7 +103,7 @@
 # Create mesh plot
 fp.plot_mesh()
 # Create denoised plot
-fp.plot(limit=160, figure_order='horizontal')
+fp.plot(figure_order='horizontal')
 fp.plot_persistence()
 
 # %% Issue