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Physiological Pipeline -> Beschreibungen verbessert
Panel Version auf die aktuellste erhöht
Unnötige Tests entfernt

pyproject.toml

@@ -9,7 +9,7 @@ license = "MIT"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.11"
 biopsykit = "^0.9.0"
-panel = "^1.3.1"
+panel = "^1.3.5"
 nilspodlib = "3.6.0"
 pandas = "1.5.2"
 numpy = "1.23.5"

src/Physiological/PHYSIOLOGICAL_CONSTANTS.py

@@ -23,7 +23,11 @@
     "while multiple Sessions describe that two or more sensors are used. \n"
 )
 
-SIGNAL_TYPE_TEXT = "# Selecting Physiological Signal Type"
+SIGNAL_TYPE_TEXT = (
+    "# Selecting Physiological Signal Type \n"
+    "Below you can select the Physiological Signal Type you want to analyse.\n"
+    "You may choose between: ECG, RSP, EEG. \n"
+)
 SELECT_CFT_TEXT = (
     "# Select CFT Sheet \n\n"
     "This step allows you to select a CFT sheet from a list "
@@ -64,7 +68,13 @@
     "hit the process button, and then proceed. "
     "Otherwise, you can skip this step and go to the next stage. \n \n"
 )
-ASK_DETECT_OUTLIER_TEXT = "# Do you want to check for outliers?"
+ASK_DETECT_OUTLIER_TEXT = (
+    "# Do you want to check for outliers? \n"
+    "If you want to check for outliers,"
+    'you can click the "Yes" button, otherwise click "Skip". In the following '
+    "step are the different kinds of outlier detection methods you can apply"
+    "to your data.\n"
+)
 
 OUTLIER_DETECTION_TEXT = (
     "# Outlier Detection \n\n"
@@ -94,11 +104,16 @@
 
 FILE_UPLOAD_TEXT = (
     "# Upload your session File \n"
-    "## The supported File formats are .bin, .csv, and you can also choose Folders.\n"
+    "## The supported File formats are .bin, .csv you can also upload Folders,"
+    "but these have to be zipped before.\n"
     "After your upload your file will also be checked if it contains the necessary columns.\n"
 )
 
-DOWNLOAD_RESULT_TEXT = "# Download Result \n"
+DOWNLOAD_RESULT_TEXT = (
+    "# Download Result \n"
+    "You can download the result of the analysis here. In the downloaded file you "
+    "you can find the analysed data as .xslsx files."
+)
 DATA_ARRIVED_TEXT = (
     "# Files uploaded successfully \n"
     "Below is a short summary of the files which you uploaded."
@@ -114,12 +129,18 @@
 ASK_ADD_TIMES_TEXT = (
     "# Do you want to add Phases for your Data?\n"
     "If you want to upload an Excel oder CSV File, or if you want to manually add Phases "
-    "to your data then click on the Add Times Button otherwise skip"
+    "to your data then click on the Add Times Button otherwise skip."
+)
+ADD_TIMES_TEXT = (
+    "# Select Times\n"
+    "In this step you can add Phases for your data. \n"
+    "You can either upload an Excel or CSV File or you can manually add "
+    "Phases for the different subjects. \n"
 )
-ADD_TIMES_TEXT = "# Select Times"
 PRESTEP_PROCESSING_TEXT = (
     "# Processing \n"
-    "Im nächsten Schritt werden die Daten verarbeitet, dieser Schritt dauert einen Moment :)."
+    "In the following step your data will be processed with the parameters you provided"
+    "in the previous steps."
 )
 
 SET_RSP_PARAMETERS_TEXT = (

src/Physiological/PhysiologicalBase.py

@@ -24,11 +24,6 @@ class PhysiologicalBase(param.Parameterized):
     estimate_rsp = param.Boolean(default=False)
     estimate_rsp_method = param.String(default="peak_trough_mean")
     freq_bands = param.Dynamic(default=None)
-    hardware = param.Selector(
-        label="Select the Hardware with which you recorded your data",
-        objects=PHYSIOLOGICAL_HW_OPTIONS,
-        default="NilsPod",
-    )
     hr_data = None
     hrv_types = param.List(default=None)
     hrv_index_name = param.Dynamic(default=None)
@@ -97,106 +92,6 @@ def get_progress(step) -> pn.indicators.Progress:
     def set_progress_value(self, step):
         self.progress.value = int((step / self.max_steps) * 100)
 
-    def select_vp_changed(self, _, event):
-        self.subject = str(event.new)
-
-    def dict_to_column(self):
-        if self.session == "Single Session" and len(self.subject_time_dict.keys()) > 1:
-            self.select_vp.options = list(self.subject_time_dict.keys())
-            self.select_vp.visible = True
-            self.select_vp.link(
-                "subject",
-                callbacks={"value": self.select_vp_changed},
-            )
-            self.subject = list(self.subject_time_dict.keys())[0]
-            self.ready = True
-        timestamps = []
-        for subject in self.subject_time_dict.keys():
-            col = pn.Column()
-            for condition in self.subject_time_dict[subject].keys():
-                cond = pn.widgets.TextInput(value=condition)
-                cond.link(
-                    (subject, condition),
-                    callbacks={"value": self.change_condition_name},
-                )
-                btn_remove_phase = pn.widgets.Button(
-                    name="Remove Phase", button_type="danger"
-                )
-                btn_remove_phase.link(
-                    (subject, condition),
-                    callbacks={"value": self.remove_btn_click},
-                )
-                col.append(pn.Row(cond, btn_remove_phase))
-                for phase, time in self.subject_time_dict[subject][condition].items():
-                    row = pn.Row()
-                    phase_name_input = pn.widgets.TextInput(value=phase)
-                    phase_name_input.link(
-                        (subject, condition, phase),
-                        callbacks={"value": self.change_phase_name},
-                    )
-                    row.append(phase_name_input)
-                    dt_picker = pn.widgets.DatetimePicker(value=time)
-                    dt_picker.link(
-                        (subject, condition, phase),
-                        callbacks={"value": self.timestamp_changed},
-                    )
-                    row.append(dt_picker)
-                    remove_btn = pn.widgets.Button(name="Remove", button_type="danger")
-                    remove_btn.link(
-                        (subject, condition, phase),
-                        callbacks={"value": self.remove_btn_click},
-                    )
-                    row.append(remove_btn)
-                    col.append(row)
-                btn_subphase = pn.widgets.Button(
-                    name="Add Subphase", button_type="primary"
-                )
-                btn_subphase.link(
-                    (subject, condition),
-                    callbacks={"value": self.add_subphase_btn_click},
-                )
-                row = pn.Row(pn.layout.HSpacer(), pn.layout.HSpacer(), btn_subphase)
-                col.append(row)
-            btn = pn.widgets.Button(name="Add Phase", button_type="primary")
-            btn.link(
-                (subject,),
-                callbacks={"value": self.add_phase_btn_click},
-            )
-            col.append(btn)
-            timestamps.append((subject, col))
-        self.times.objects = [pn.Accordion(objects=timestamps)]
-
-    def add_phase_btn_click(self, target, _):
-        new_phase_name = "New Phase"
-        self.subject_time_dict[target[0]][new_phase_name] = pd.Series(
-            {"New Subphase": datetime.datetime.now()}
-        )
-        active = self.times.objects[0].active
-        self.dict_to_column()
-        self.times.objects[0].active = active
-
-    def add_subphase_btn_click(self, target, event):
-        new_phase_name = "New Subphase"
-        if new_phase_name in list(
-            self.subject_time_dict[target[0]][target[1]].index.values
-        ):
-            i = 1
-            new_phase_name = new_phase_name + " " + str(i)
-            while new_phase_name in list(
-                self.subject_time_dict[target[0]][target[1]].index.values
-            ):
-                i += 1
-                new_phase_name = new_phase_name + " " + str(i)
-        self.subject_time_dict[target[0]][target[1]] = pd.concat(
-            [
-                self.subject_time_dict[target[0]][target[1]],
-                pd.Series(data=[datetime.datetime.now()], index=[new_phase_name]),
-            ]
-        )
-        active = self.times.objects[0].active
-        self.dict_to_column()
-        self.times.objects[0].active = active
-
     def get_outlier_params(self):
         if self.skip_outlier_detection:
             self.outlier_params = None

src/Physiological/file_upload.py

@@ -47,7 +47,6 @@ def __init__(self, **params):
         self.update_step(4)
         self.select_timezone.link(self, callbacks={"value": self.timezone_changed})
         self.select_hardware.link(self, callbacks={"value": self.hardware_changed})
-        self._select_hardware = pn.widgets.Select.from_param(self.param.hardware)
         self.file_input.link(
             self,
             callbacks={
@@ -77,6 +76,9 @@ def timezone_changed(self, _, event):
             self.ready = True
 
     def hardware_changed(self, _, event):
+        if event.new not in self.select_hardware.options:
+            self.select_hardware.value = self.select_hardware.options[0]
+            return
         self.hardware = event.new
         if self.hardware == "NilsPod":
             self.file_input.accept = ".csv,.bin, .zip"