Revamp CLI

rsHRF/rsHRF_GUI/datatypes/misc/parameters.py

@@ -2,6 +2,7 @@
 import numpy as np
 from copy import deepcopy
 from ...misc.status import Status
+from ....utils.default_parameters import default_parameters
 
 
 class Parameters:
@@ -12,31 +13,11 @@ class Parameters:
 
     def __init__(self):
         # initialize default parameters
-        self.estimation = "canon2dd"
-        self.passband = [0.01, 0.08]
-        self.passband_deconvolve = [0.0, sys.float_info.max]
-        self.TR = 2.0
-        self.localK = 1
-        self.T = 3
-        self.T0 = 1
-        self.TD_DD = 2
-        self.AR_lag = 1
-        self.thr = 1
-        self.order = 3
-        self.volterra = 0
-        self.len = 24
-        self.temporal_mask = []
-        self.min_onset_search = 4
-        self.max_onset_search = 8
-        self.dt = self.TR / self.T
-        self.lag = np.arange(
-            np.fix(self.min_onset_search / self.dt),
-            np.fix(self.max_onset_search / self.dt) + 1,
-            dtype="int",
-        )
+        for key, value in default_parameters.items():
+            setattr(self, key, value)
 
     # getters
-    def get_estimation(self):
+    def get_estimation(self) -> str:
         return self.estimation
 
     def get_passband(self):
@@ -281,7 +262,7 @@ def set_Volterra(self, volterra):
         """
         Sets Volterra if the estimation rule is canon2dd
         """
-        if self.estimation == "canon":
+        if "canon" in self.estimation:
             try:
                 volterra = int(volterra)
             except:
@@ -373,8 +354,8 @@ def update_lag(self):
         Re-calculating lag
         """
         self.lag = np.arange(
-            np.fix(self.min_onset_search / self.dt),
-            np.fix(self.max_onset_search / self.dt) + 1,
+            np.trunc(self.min_onset_search / self.dt),
+            np.trunc(self.max_onset_search / self.dt) + 1,
             dtype="int",
         )
 

rsHRF/rsHRF_GUI/gui_windows/inputWindow.py

@@ -11,6 +11,7 @@
     StringVar,
     Label,
 )
+from ...utils.default_parameters import available_estimations
 
 
 class InputWindow:
@@ -146,14 +147,7 @@ def getOutputDir():
         maskFileLabel = Label(window, text="")
         outputPathLabel = Label(window, text="")
         estimationDropDown = OptionMenu(
-            window,
-            self.estimationOption,
-            "canon2dd",
-            "sFIR",
-            "FIR",
-            "gamma",
-            "fourier",
-            "fourier w/ hanning",
+            window, self.estimationOption, *available_estimations
         )
         # placing widgets
         inputFormat.grid(row=0, column=0, padx=(5, 5), pady=(5, 5))

rsHRF/rsHRF_GUI/gui_windows/main.py

@@ -13,7 +13,7 @@
 
 
 class Main:
-    def __init__(self):
+    def __init__(self, parameters=None):
         # main window
         root = Tk()
         root.title("rsHRF Toolbox")
@@ -46,7 +46,9 @@ def __init__(self):
         input = ()  # receives the input from the input window
         output = {}  # receives the output from the core
         # initializing parameter window
-        parameter_window.setParameters(core.get_parameters())
+        parameter_window.setParameters(
+            parameters if parameters is not None else core.get_parameters()
+        )
         parameter_window.display()
 
         """ Gets the input from the input toplevel.

rsHRF/rsHRF_GUI/gui_windows/parameterWindow.py

@@ -7,8 +7,8 @@ def __init__(self):
         self.window = Toplevel()
         self.window.title("Parameters")
         self.parameters = {}
-        self.labels = []
-        self.entries = []
+        self.labels: list[Label] = []
+        self.entries: list[Entry] = []
         # get screen width and height
         screen_width = self.window.winfo_screenwidth()
         screen_height = self.window.winfo_screenheight()

rsHRF/rsHRF_GUI/run.py

@@ -1,5 +1,5 @@
 from .gui_windows.main import Main
 
 
-def run():
-    Main()
+def run(parameters=None):
+    Main(parameters)