Fix bug with plotting time axis for fitters.

examples/Controlling-Glucose-Metabolis-in-Yeast.ipynb

@@ -1383,16 +1383,6 @@
     "**In conclusion,** this was an eye-opening and very interesting class that is unlike anything I've taken before. I sincerely apologize for not being able to attend class in-person during some of the final weeks and for getting HW2 in late; I have had a lot of family issues happening this quarter and I had to fly home for the weekend HW2 was due when I missed your email. It's just been a stressful quarter with 4 classes and starting/trying to perform well in my new lab. I found this class to be very valuable and it has motivated me to take some classes in systems biology and more classes in biomodeling/biostatistics/computational biology. I hope there comes a time when I can apply this to my own research during graduate school, especially now that I've got a great pipeline to design & test simple controls. Thank you so much, Professor Hellerstein, I hope to see you around. Best of luck with your research & other classes!"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "bf9d5e39-4e93-4cfb-ba13-476d0d084b35",
-   "metadata": {
-    "id": "3001497a-1a07-47c5-9a0a-c6ad0da88035"
-   },
-   "source": [
-    "P.S. I restarted my kernel on JupyterHub & ran all cells and verified that each one worked before submission per your advice from HW1. Please let me know if there is anything that doesn't work for you."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

src/controlSBML/control_sbml.py

@@ -148,7 +148,7 @@ def __init__(self, model_reference:str,
                  fitter_method:Optional[str]=OPTION_DCT[cn.O_FITTER_METHOD],
                  setpoint:Optional[float]=OPTION_DCT[cn.O_SETPOINT],
                  sign:Optional[int]=OPTION_DCT[cn.O_SIGN],
-                 times:Optional[np.ndarray[float]]=OPTION_DCT[cn.O_TIMES],
+                 times:Optional[np.ndarray[float]]=None,
                  save_path:Optional[str]=SAVE_PATH,
                  **kwargs):
         """
@@ -437,7 +437,7 @@ def _initializeStaircaseOptions(self, initial_value=None, final_value=None, num_
 
     ############ PLOTTERS ##############
     def plotModel(self, 
-                  times:Optional[np.ndarray[float]]=OPTION_DCT[cn.O_TIMES],
+                  times:Optional[np.ndarray[float]]=None,
                   selections:Optional[List[str]]=OPTION_DCT[cn.O_SELECTIONS],
                   **kwargs)->ModelResult:
         """
@@ -473,7 +473,7 @@ def plotStaircaseResponse(self,
                               initial_value:Optional[float]=OPTION_DCT[cn.O_INITIAL_VALUE],
                               final_value:Optional[float]=OPTION_DCT[cn.O_FINAL_VALUE],
                               num_step:Optional[int]=OPTION_DCT[cn.O_NUM_STEP],
-                              times:Optional[np.ndarray]=OPTION_DCT[cn.O_TIMES],
+                              times:Optional[np.ndarray]=None,
                               **kwargs)->StaircaseResponseResult:
         """
         Simulates the staircase response and plots it.
@@ -514,7 +514,7 @@ def plotTransferFunctionFit(self,
             final_value:Optional[float]=None,
             num_step:Optional[int]=OPTION_DCT[cn.O_NUM_STEP],
             fitter_method:Optional[str]=OPTION_DCT[cn.O_FITTER_METHOD],
-            times:Optional[np.ndarray]=OPTION_DCT[cn.O_TIMES],
+            times:Optional[np.ndarray]=None,
             **kwargs)->TransferFunctionFitResult:
         """
         Simulates the staircase response and plots it. Sets the fitter result.
@@ -585,7 +585,7 @@ def _plotClosedLoop(self,
                         setpoint:Optional[float]=OPTION_DCT[cn.O_SETPOINT],
                         sign:Optional[float]=OPTION_DCT[cn.O_SIGN],
                         selections:Optional[List[str]]=OPTION_DCT[cn.O_SELECTIONS],
-                        times:Optional[np.ndarray]=OPTION_DCT[cn.O_TIMES],
+                        times:Optional[np.ndarray]=None,
                         **kwargs):
         """
         Plots the closed loop response. Control parameters not explicity specified are None.
@@ -628,7 +628,7 @@ def plotGridDesign(self,
                        grid:Grid,
                        setpoint:Optional[float]=OPTION_DCT[cn.O_SETPOINT],
                        sign:Optional[float]=OPTION_DCT[cn.O_SIGN],
-                       times:Optional[np.ndarray]=OPTION_DCT[cn.O_TIMES],
+                       times:Optional[np.ndarray]=None,
                        num_process:Optional[int]=OPTION_DCT[cn.O_NUM_PROCESS],
                        num_restart:Optional[int]=OPTION_DCT[cn.O_NUM_RESTART],
                        selections:Optional[List[str]]=OPTION_DCT[cn.O_SELECTIONS],
@@ -713,7 +713,7 @@ def plotDesign(self,
                 kF_spec:bool=OPTION_DCT[cn.O_KF_SPEC],
                 setpoint:Optional[float]=OPTION_DCT[cn.O_SETPOINT],
                 sign:Optional[float]=OPTION_DCT[cn.O_SIGN],
-                times:Optional[np.ndarray]=OPTION_DCT[cn.O_TIMES],
+                times:Optional[np.ndarray]=None,
                 num_process:Optional[int]=OPTION_DCT[cn.O_NUM_PROCESS],
                 num_restart:Optional[int]=OPTION_DCT[cn.O_NUM_RESTART],
                 selections:Optional[List[str]]=OPTION_DCT[cn.O_SELECTIONS],

src/controlSBML/siso_transfer_function_fitter.py

@@ -56,7 +56,8 @@ def __init__(self, timeseries:Timeseries, num_zero:Optional[int]=0, num_pole:Opt
         self.out_std = np.std(self.out_arr)
         self.max_out_value = np.max(self.out_arr)
         self.dt = np.round(np.mean(np.diff(timeseries.index)))/cn.MS_IN_SEC
-        self.times = np.array([self.dt*n for n in range(len(timeseries.index))])  # Must be evenly spaced
+        start_time = timeseries.index[0]/cn.MS_IN_SEC
+        self.times = start_time + np.array([self.dt*n for n in range(len(timeseries.index))])  # Must be evenly spaced
         self.times = np.reshape(self.times, (len(self.times),))
         self.length = len(self.times)
         self.num_zero:int = num_zero  # type: ignore