allow basis parameter override in smooth plot

fixed bug that would exclude step key = 0 -
TangleSpace · Mar 21, 2021 · 5fb8a4a · 5fb8a4a
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diff --git a/README.md b/README.md
@@ -21,7 +21,6 @@ It's all about tools that just work and no need for extensive knowledge of Panda
 </p>
 
 ## Installation
-
 HotStepper can be installed from PyPI:
 
 ```bash
@@ -32,7 +31,6 @@ Conda install coming soon!
 
 
 ## Quick Test Drive
-
 <p align="center">
 	<a href="https://mybinder.org/v2/gh/TangleSpace/hotstepper/master?filepath=docs%2Fexamples" alt="Binder">
         <img src="https://mybinder.org/badge_logo.svg" /></a>
@@ -52,6 +50,7 @@ I'd like to thank the Staircase package owner for currating some of these datase
 
 ## Step Functions
 Behold! the power of the [Heaviside step function](https://en.wikipedia.org/wiki/Heaviside_step_function)
+Checkout a detailed, somewhat, probably <a href="https://hotstepper.readthedocs.io/notebooks/step_functions.html">very exciting, non-stop adventure ride</a> of through some of the, umm, math.....behind HotStepper and step functions. With any luck, someone will have a deadline tomorrow and HotStepper and step functions will save the day! Or atleast, I like to keep thinking that.
 
 ### Ok, don't packup just yet.
 <p align="center"><img src="https://raw.githubusercontent.com/tanglespace/hotstepper/master/docs/images/temperature.gif" title="Daily Temperature" alt="Daily Temperature", width="50%" height="50%"><img src="https://raw.githubusercontent.com/tanglespace/hotstepper/master/docs/images/store.gif" title="Store" alt="Store", width="50%" height="50%"></p>

diff --git a/docs/basis.rst b/docs/basis.rst
@@ -108,14 +108,24 @@ Bases
             :nowrap:
 
             \begin{equation*}
-            \gamma(t,\alpha) =1-exp\left(-\frac{t}{\alpha} \right)
+            \gamma(t,\alpha) =exp\left(-exp\left(-\frac{t}{\alpha} \right)\right)
             \;\;\;\;\; where \;t,\; \alpha \in \mathbb{R}
             \end{equation*}
+
+     - Normal
+        .. math::
+            :nowrap:
+
+            \begin{equation*}
+            \gamma(t,\alpha) =exp\left(-\frac{t^2}{\alpha} \right)
+            \;\;\;\;\; where \;t,\; \alpha \in \mathbb{R}
+            \end{equation*}
+
      - Sinc
         .. math::
             :nowrap:
 
             \begin{equation*}
-            \gamma(t,\alpha) =\frac{sin\left(\frac{t}{\alpha} \right)}{\left(\frac{t}{\alpha} \right)}
+            \gamma(t,\alpha) =\frac{sin\left(\frac{t}{\alpha} \right)}{\left(t \right)}
             \;\;\;\;\; where \;t,\; \alpha \in \mathbb{R}
             \end{equation*}
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -8,5 +8,4 @@ Case Studies
    examples/more currency
    examples/uber trips
    examples/daily temperatures
-   examples/store_orders
-   examples/sequency_quickstart
+   examples/store_orders
diff --git a/docs/examples/more currency.ipynb b/docs/examples/more currency.ipynb
diff --git a/docs/images/sad.jpg b/docs/images/sad.jpg
diff --git a/docs/index.rst b/docs/index.rst
@@ -32,21 +32,25 @@ Behold! the power of the `Heaviside step function <https://en.wikipedia.org/wiki
 .. rst-class:: center
 
 HotStepper is a Numpy based step function analysis and exploration library that trys (not always) to follow general patterns established by Numpy in order to implement step and smoothing functions by way of a linear algebra approach.
-
 Some use cases for the HotStepper package are the analysis of count and discontinuous data (queues, forex, trips etc.). It's all about tools that just work and no need for extensive knowledge of Pandas or Numpy or whatever, just HotStepper. Analysis and exploration should take less code!
 
-Sequency Analysis
+**Step Functions**
 ======================================
+.. toctree::
+   :maxdepth: 1
 
+   step_functions.rst
+
+**Sequency Analysis**
+======================================
 .. toctree::
    :maxdepth: 1
 
    sequency_methods.rst
    sequency.rst
 
-What do you want to know?
+**What do you want to know?**
 ======================================
-
 .. toctree::
    :maxdepth: 1
 

diff --git a/docs/notebooks/Even more How To's.ipynb b/docs/notebooks/Even more How To's.ipynb
diff --git a/docs/notebooks/How To's.ipynb b/docs/notebooks/How To's.ipynb
diff --git a/docs/notebooks/More How To's.ipynb b/docs/notebooks/More How To's.ipynb
diff --git a/docs/notebooks/prettyplot.ipynb b/docs/notebooks/prettyplot.ipynb
diff --git a/docs/notebooks/sequency_basics.ipynb b/docs/notebooks/sequency_basics.ipynb
@@ -308,9 +308,9 @@
    "source": [
     "Wait, I thought we were talking about Sequency Analysis, what is the Walsh transform? In the realm of Sequency Analysis, the Walsh transform plays the role of the Fourier transform, with a few differences. It is those delicious differences that make this investigation worth the effort, as the Fourier transform is awesome, no doubt, but it does have some hang ups if we give it data that doesn't play nicely in terms of smoothness and jumpiness? is that a word, it is now. We will have a look at the younger but less well known brother of the Fourier transform, the Welsh transform and will show how whilst Fourier is all that and a bag of potato chips, there are some cases (actually quite a few) where we should use a different method and will be rewarded with more insight and a clearer picture of the nature of the data. Anyways, enough woffling.\n",
     "\n",
-    "The Walsh transform is defined as the sequency ordered Hadamand transform, which is nothing more than a matrix full of -1 and 1's arranged in order of increasing sequency number. Ok ok, sequency number, wtf is that? If we start with the definition of [frequency](https://en.wikipedia.org/wiki/Frequency#:~:text=Frequency%20is%20the%20number%20of,a%20repeating%20event%20per%20second.), in simple terms, the number of times a pattern repeats within an interval, usually a unit interval of time, such as a second and is defined as;\n",
+    "The Walsh transform is defined as the sequency ordered Hadamand transform, which is nothing more than a matrix full of -1 and 1's arranged in order of increasing sequency number. Ok ok, sequency number, wtf is that? If we start with the definition of [frequency](https://en.wikipedia.org/wiki/Frequency#:~:text=Frequency%20is%20the%20number%20of,a%20repeating%20event%20per%20second.), in simple terms, the number of times a pattern repeats within an interval T, usually a unit interval of time, such as a second and is defined as;\n",
     "\n",
-    "$f = \\frac{1}{T} \\;\\; T = 1 \\;time \\;unit \\;(usually \\;seconds)$\n",
+    "$f = \\frac{1}{T}$\n",
     "\n",
     "Fair enough, so the definition of [sequency](https://mathworld.wolfram.com/Sequency.html) is similar, except we just use the idea of crossing **through** zero, the number of zero crossings within a given interval.\n",
     "\n",

diff --git a/docs/notebooks/step_functions.ipynb b/docs/notebooks/step_functions.ipynb
diff --git a/docs/step_functions.rst b/docs/step_functions.rst
@@ -0,0 +1,16 @@
+Step Functions
+======================================
+
+.. warning::
+
+    The content ahead may cause extreme drowsiness or deplete the will to go on.
+
+    .. image:: images/sad.jpg
+       :width: 50%
+       :alt: sad warning
+       :align: left
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/step_functions.ipynb
diff --git a/docs/steps_methods.rst b/docs/steps_methods.rst
@@ -25,7 +25,7 @@ Basic methods
 
 .. _api.plot_functions:
 
-Plotting functions
+Plotting methods
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autosummary::
    :toctree: api/
@@ -42,7 +42,7 @@ Plotting functions
 
 .. _api.class_loader_functions:
 
-Class Loader functions
+Class Loader methods
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
@@ -54,7 +54,7 @@ Class Loader functions
 
 .. _api.instant_loader_functions:
 
-Instance Loader functions
+Instance Loader methods
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
@@ -66,7 +66,7 @@ Instance Loader functions
 
 .. _api.step_functions:
 
-Step Functions
+Step methods
 ~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
@@ -145,7 +145,7 @@ Summary statistics
    Steps.histogram
 
 
-Miscellaneous functions
+Miscellaneous methods
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::

diff --git a/hotstepper/__init__.py b/hotstepper/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '1.0.9'
+__version__ = '1.0.10'
 __packagename__ = 'HotStepper'
 __author__ = 'Jackson Storm'
 

diff --git a/hotstepper/basis/Bases.py b/hotstepper/basis/Bases.py
@@ -16,10 +16,11 @@ class Bases(ABC):
     The mathematical bases defined within this class are;
 
     Heaviside
-    Logit
+    Logistic
     Sigmoid
     Arctan
     Exponential
+    Normal
     Sinc
     
     """
@@ -70,11 +71,21 @@ def sigmoid(x,steps,param):
 
     @staticmethod
     @njit(parallel=True,nogil=True)
-    def expon(x,steps,param):
+    def exponential(x,steps,param):
         result = np.zeros(len(x))
 
         for i in nb.prange(steps.shape[0]):
-            result += steps[i,2]*(1.0 - np.exp(-1*steps[i,1]*(x-steps[i,0])/param))
+            result += steps[i,2]*(np.exp(-1*np.exp(-1*steps[i,1]*(x-steps[i,0])/param)))
+
+        return result
+
+    @staticmethod
+    @njit(parallel=True,nogil=True)
+    def normal(x,steps,param):
+        result = np.zeros(len(x))
+
+        for i in nb.prange(steps.shape[0]):
+            result += steps[i,2]*(np.exp((-1/param)*(steps[i,1]*(x-steps[i,0]))**2))
 
         return result
 
@@ -85,7 +96,7 @@ def sinc(x,steps,param):
         result = np.zeros(len(x))
 
         for i in nb.prange(steps.shape[0]):
-            result += steps[i,2]*np.sinc(steps[i,1]*(x-steps[i,0])/param)
+            result += steps[i,2]*(np.sinc(steps[i,1]*(x-steps[i,0])/param))/param
 
         return result
 

diff --git a/hotstepper/core/AbstractSteps.py b/hotstepper/core/AbstractSteps.py
@@ -366,12 +366,18 @@ def smooth_step(self,xdata,smooth_factor = None,smooth_basis = None, process_inp
         using_default = self._basis.name == 'Heaviside'
         #check we don't already have a new basis assigned
         if using_default:
-            if smooth_factor is None:
-                smooth_factor = self._get_auto_smooth_factor()
+
 
             if smooth_basis is None:
+                if smooth_factor is None:
+                    smooth_factor = self._get_auto_smooth_factor()
                 self.rebase(new_basis=Basis(Bases.logistic,param=smooth_factor))
             else:
+                # Override basis param is we got smooth_factor
+                if smooth_factor is not None:
+                    smooth_basis.param = smooth_factor
+                    #smooth_factor = self._get_auto_smooth_factor()
+
                 self.rebase(new_basis=smooth_basis)
 
         if self._step_data.shape[0] > 0:
@@ -408,14 +414,19 @@ def reflect(self,reflect_point = 0):
 
 
     def __iter__(self):
-        self._index = 0
-        return iter([type(self)(self._using_dt).add_steps([s]) for s in self._step_data])
+
+        if self._step_data[0,DataModel.START.value] == get_epoch_start(False):
+            self._index = 1
+            return iter([type(self)(self._using_dt).add_steps([s]) for s in self._step_data[1:]])
+        else:
+            self._index = 0
+            return iter([type(self)(self._using_dt).add_steps([s]) for s in self._step_data])
 
 
     def __next__(self):
         if self._index < self._step_data.shape[0]:
             self._index += 1
-            return type(self)(self._using_dt).add_steps(self._step_data[self._index-1])
+            return type(self)(self._using_dt).add_steps([self._step_data[self._index-1]])
         else:
             self._index = 0
             raise StopIteration

diff --git a/hotstepper/core/Steps.py b/hotstepper/core/Steps.py
@@ -234,7 +234,7 @@ def add(self,steps):
     def _recalculate(self):
         try:
             self._step_data = self._step_data[~np.isnan(self._step_data[:,DataModel.START.value])]
-            self._step_data = self._step_data[self._step_data[:,DataModel.START.value]!=0]
+            #self._step_data = self._step_data[self._step_data[:,DataModel.START.value]!=0]
             self._step_data = self._step_data[self._step_data[:,DataModel.START.value]!=np.NINF]
             self._step_data = self._step_data[self._step_data[:,DataModel.START.value]!=np.PINF]
             self._step_data = self._step_data[np.argsort(self._step_data[:,DataModel.START.value])]

diff --git a/hotstepper/mixins/StepsPlottingMixin.py b/hotstepper/mixins/StepsPlottingMixin.py
@@ -63,17 +63,18 @@ def smooth_plot(self,smooth_factor = None,smooth_basis=None, interval = 0.01,ax=
         Matplotlib.Axes
             A reference to the plot axes object to allow further plotting on the same axes.
 
-        """
-        # Examples
-        # ==========
+        Examples
+        ==========
 
-        # .. plot::
-        #     :context: close-figs
+        .. plot::
+            :context: close-figs
 
-        #     st = Step(5,10,3) + Step(6,weight=2)
-        #     ax = st.smooth_plot(smooth_factor=2,offset=0.01)
-        #     st.plot(ax=ax,color='g')
-        #     ax.set_title('Smooth Steps Plot')
+            st = Step(5,10,3) + Step(6,weight=2)
+            ax = st.smooth_plot(smooth_factor=2)
+            st.plot(ax=ax,color='g')
+            ax.set_title('Smooth Steps Plot')
+
+        """
 
         return self.plot(method='smooth',smooth_factor = smooth_factor,smooth_basis=smooth_basis,interval = interval,ax=ax,where=where,**kargs)
 
@@ -111,22 +112,24 @@ def plot(self,method=None,smooth_factor=None,smooth_basis=None,interval = 0.01,a
         Matplotlib.Axes
             A reference to the plot axes object to allow further plotting on the same axes.
 
-        """
-
-        # Examples
-        # ==========
+        Examples
+        ==========
 
-        # .. plot::
-        #     :context: close-figs
+        .. plot::
+            :context: close-figs
 
-        #     s1 = Step(5,10,3)
-        #     s2 = Step(6,weight=2)
-        #     st = s1 + s2
-        #     ax = s1.plot(color='r')
-        #     s2.plot(ax=ax,color='g',method='function')
-        #     st.plot(ax=ax)
+            s1 = Step(5,10,3)
+            s2 = Step(6,weight=2)
+            st = s1 + s2
+            ax = s1.plot(color='r',figsize=(8,4))
+            s2.plot(ax=ax,method='function')
+            s2.plot(ax=ax,method='smooth')
+            st.plot(ax=ax)
+            st.smooth_plot(ax=ax)
 
-        #     ax.set_title('Steps Plot')
+            ax.set_title('Steps Plot')
+            
+        """
 
         if ax is None:
             plot_size = kargs.pop('figsize',None)

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name='hotstepper',
-    version='1.0.9',
+    version='1.0.10',
     description='Numpy based step function library.',
     long_description=long_description,
     long_description_content_type='text/markdown',
@@ -24,12 +24,10 @@
     packages=setuptools.find_packages(),
     classifiers=[
         'Operating System :: OS Independent',
-        'Intended Audience :: Science/Research/Analysis',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
-        'Topic :: Scientific/Engineering/Analysis',
     ],
     install_requires=[
         'numpy',