Merge pull request #80 from tgrbrooks/condition-replicates

Condition replicates

Author: tgrbrooks

ada/components/data_list_item.py

@@ -17,7 +17,6 @@ def __init__(self, text, index, parent=None):
         del_button.clicked.connect(parent.remove_item)
         add_button = AddButton()
         add_button.clicked.connect(parent.add_to_item)
-        add_button.clicked.connect(parent.update_data_list)
         label = QLabel(text)
         label.setStyleSheet(styles.default_font_bold)
 
@@ -31,25 +30,24 @@ def __init__(self, text, index, parent=None):
         hwidget.setLayout(layout)
         vlayout = QVBoxLayout()
         vlayout.addWidget(hwidget)
-        if(data_manager.num_replicates(index) > 1):
-            for j in range(1, data_manager.num_replicates(index), 1):
-                hlayout = QHBoxLayout()
-                hlayout.addWidget(QLabel('-'))
-                sub_del_button = DeleteButton()
-                hlayout.addWidget(sub_del_button)
-                sub_del_button.clicked.connect(
-                    lambda: parent.remove_replicate(j)
-                )
-                inner_label = QLabel(
-                    data_manager.growth_data.replicate_files[index][j].label
-                )
-                inner_label.setStyleSheet(styles.small_font)
-                hlayout.addWidget(inner_label)
-                hlayout.addStretch()
-                hlayout.setSizeConstraint(QLayout.SetFixedSize)
-                subwidget = QWidget()
-                subwidget.setLayout(hlayout)
-                vlayout.addWidget(subwidget)
+        for j in range(1, data_manager.num_replicates(index), 1):
+            hlayout = QHBoxLayout()
+            hlayout.addWidget(QLabel('-'))
+            sub_del_button = DeleteButton()
+            hlayout.addWidget(sub_del_button)
+            sub_del_button.clicked.connect(
+                lambda: parent.remove_replicate(j)
+            )
+            inner_label = QLabel(
+                data_manager.growth_data.replicate_files[index][j].label
+            )
+            inner_label.setStyleSheet(styles.small_font)
+            hlayout.addWidget(inner_label)
+            hlayout.addStretch()
+            hlayout.setSizeConstraint(QLayout.SetFixedSize)
+            subwidget = QWidget()
+            subwidget.setLayout(hlayout)
+            vlayout.addWidget(subwidget)
         vlayout.setSpacing(0)
         vlayout.setContentsMargins(0, 0, 0, 0)
         vlayout.addStretch()
@@ -61,23 +59,47 @@ def __init__(self, text, index, parent=None):
 
 class ConditionListItem():
 
-    def __init__(self, text, parent=None):
+    def __init__(self, text, index, parent=None):
         self.item = QListWidgetItem()
         self.widget = QWidget()
         del_button = DeleteButton()
         del_button.clicked.connect(parent.remove_condition_item)
         label = QLabel(text)
         label.setStyleSheet(styles.default_font_bold)
 
+        hwidget = QWidget()
         layout = QHBoxLayout()
         layout.addWidget(del_button)
         layout.addWidget(label)
         layout.addStretch()
         layout.setSizeConstraint(QLayout.SetFixedSize)
-        layout.setSpacing(5)
-        layout.setContentsMargins(10, 10, 5, 5)
+        hwidget.setLayout(layout)
+        vlayout = QVBoxLayout()
+        vlayout.addWidget(hwidget)
+        for j in range(1, data_manager.num_condition_replicates(index), 1):
+            hlayout = QHBoxLayout()
+            hlayout.addWidget(QLabel('-'))
+            sub_del_button = DeleteButton()
+            hlayout.addWidget(sub_del_button)
+            sub_del_button.clicked.connect(
+                lambda: parent.remove_condition_replicate(j)
+            )
+            inner_label = QLabel(
+                data_manager.condition_data.replicate_files[index][j].label
+            )
+            inner_label.setStyleSheet(styles.small_font)
+            hlayout.addWidget(inner_label)
+            hlayout.addStretch()
+            hlayout.setSizeConstraint(QLayout.SetFixedSize)
+            subwidget = QWidget()
+            subwidget.setLayout(hlayout)
+            vlayout.addWidget(subwidget)
+        vlayout.setSpacing(0)
+        vlayout.setContentsMargins(0, 0, 0, 0)
+        vlayout.addStretch()
+        vlayout.setSizeConstraint(QLayout.SetFixedSize)
 
-        self.widget.setLayout(layout)
+        self.widget.setLayout(vlayout)
         self.item.setSizeHint(self.widget.sizeHint())
 
 

ada/data/data_manager.py

@@ -4,7 +4,7 @@
 # Local includes
 from ada.data.algae_data import AlgaeData
 from ada.data.data_holder import DataHolder
-from ada.data.processor import process_data, time_average, average_data
+from ada.data.processor import process_data, time_average, time_average_arrays, average_data
 from ada.data.models import get_model
 import ada.configuration as config
 from ada.logger import logger
@@ -71,6 +71,9 @@ def has_replicates(self, index):
     def num_replicates(self, index):
         return len(self.growth_data.replicate_files[index])
 
+    def num_condition_replicates(self, index):
+        return len(self.condition_data.replicate_files[index])
+
     def get_replicate_data(self, i, j, xvar, yvar):
         xdata = self.growth_data.replicate_files[i][j].get_xdata(xvar)
         ydata = self.growth_data.replicate_files[i][j].get_ydata(
@@ -156,13 +159,15 @@ def get_growth_legend(self, i, label_names=None, extra_info=None, only_extra=Fal
             legend_label = self.growth_data.data_files[i].get_header_info(extra_info)
         return legend_label
 
-    def get_condition_xy_data(self, i, cond_name, xvar=None, condition_average=None):
+    def get_condition_xy_data(self, i, cond_name, xvar=None, condition_average=None, std_err=False):
         if xvar is None:
             xvar = config.xvar
         if condition_average is None:
             condition_average = config.condition_average
+        if config.std_err:
+            std_err = True
 
-        for cond in self.condition_data.data_files:
+        for j, cond in enumerate(self.condition_data.data_files):
             if self.growth_data.data_files[i].reactor != cond.reactor:
                 continue
             if self.growth_data.data_files[i].sub_reactor != cond.sub_reactor:
@@ -171,12 +176,7 @@ def get_condition_xy_data(self, i, cond_name, xvar=None, condition_average=None)
                 continue
             if self.growth_data.data_files[i].time != cond.time:
                 continue
-            xdata = cond.get_xdata(xvar)
-            ydata = cond.get_signal(cond_name)
-            if condition_average != -1:
-                xdata, ydata, _ = time_average(
-                    xdata, ydata, condition_average)
-            return xdata, ydata
+            return self.get_condition_data(j, xvar, cond_name, condition_average, std_err)
         raise RuntimeError('No condition data found for %s'
                            % (self.growth_data.data_files[i].name))
 
@@ -188,16 +188,29 @@ def get_condition_data(self, i, xvar=None, yvar=None, condition_average=None, st
         if condition_average is None:
             condition_average = config.condition_average
         if config.std_err:
-            std_err = True
+            std_err = config.std_err
 
-        xdata = self.condition_data.data_files[i].get_xdata(xvar)
-        ydata = self.condition_data.data_files[i].get_signal(yvar)
+        xdatas = []
+        ydatas = []
+        for rep in self.condition_data.replicate_files[i]:
+            xdata = rep.get_xdata(xvar)
+            ydata = rep.get_ydata(yvar)
+            xdatas.append(xdata)
+            ydatas.append(ydata)
         yerr = None
         # Average condition data over time
-        if(condition_average != -1):
-            # Do something
+        if len(xdatas) > 1 and condition_average != -1:
+            xdata, ydata, yerr = \
+                time_average_arrays(xdatas, ydatas, condition_average, std_err)
+        elif len(xdatas) > 1:
+            xdata, ydata, yerr = average_data(xdatas, ydatas, std_err)
+        elif len(xdatas) == 1 and condition_average != -1:
             xdata, ydata, yerr = \
-                time_average(xdata, ydata, condition_average, std_err)
+                time_average(xdatas[0], ydatas[0], condition_average, std_err)
+        elif len(xdatas) == 1:
+            return xdatas[0], ydatas[0], None
+        else:
+            raise RuntimeError('No condition data found at index %i' % i)
         return xdata, ydata, yerr
 
     def get_condition_ytitle(self, i, yvar=None, yname=None, yunit=None):
@@ -279,7 +292,7 @@ def get_averages(self, cond_name, start_t, end_t):
         averages = []
         errors = []
         for i, _ in enumerate(self.growth_data.data_files):
-            xdata, ydata = self.get_condition_xy_data(i, cond_name)
+            xdata, ydata, _ = self.get_condition_xy_data(i, cond_name)
             dat = np.array([])
             for i, x in enumerate(xdata):
                 if x >= start_t and x <= end_t:
@@ -300,7 +313,7 @@ def get_condition_at(self, cond_name, time):
         logger.debug('Getting condition %s at time %.2f' % (cond_name, time))
         values = []
         for i, _ in enumerate(self.growth_data.data_files):
-            xdata, ydata = self.get_condition_xy_data(i, cond_name)
+            xdata, ydata, _ = self.get_condition_xy_data(i, cond_name)
             values.append(np.interp(time, xdata, ydata))
         return values
 

ada/data/processor.py

@@ -165,7 +165,7 @@ def time_average(xdata, ydata, window, show_err=False):
     while(i < len(xdata)):
         data_x = np.array([])
         data_y = np.array([])
-        while(i < len(xdata) and xdata[i] < w_i*window):
+        while(i < len(xdata) and xdata[i] < w_i * window):
             data_x = np.append(data_x, xdata[i])
             data_y = np.append(data_y, ydata[i])
             i = i + 1
@@ -186,6 +186,44 @@ def time_average(xdata, ydata, window, show_err=False):
         w_i = w_i + 1
     return new_xdata, new_ydata, new_yerr
 
+# Function to average arrays of data over time period
+def time_average_arrays(xdatas, ydatas, window, show_err=False):
+    logger.debug('Averaging data over time window of %i' % window)
+    new_xdata = np.array([])
+    new_ydata = np.array([])
+    new_yerr = np.array([])
+    w_i = 1
+    data_remaining = True
+    while data_remaining:
+        window_x = np.array([])
+        window_y = np.array([])
+        finished = True
+        for i, xdata in enumerate(xdatas):
+            # Check if there's any data in the next window
+            if len(xdata[xdata >= (w_i) * window]) > 0:
+                finished = False
+            mask = ((xdata >= (w_i - 1) * window) & (xdata < w_i * window))
+            window_x = np.append(window_x, xdata[mask])
+            window_y = np.append(window_y, ydatas[i][mask])
+        if finished:
+            data_remaining = False
+        if(window_y.size == 0):
+            w_i = w_i + 1
+            continue
+        mean_x = np.mean(window_x)
+        mean_y = np.mean(window_y)
+        std_dev = np.std(window_y, ddof=1)
+        if(show_err):
+            std_dev = std_dev/np.sqrt(window_y.size)
+        new_xdata = np.append(new_xdata, mean_x)
+        new_ydata = np.append(new_ydata, mean_y)
+        if(window_y.size == 1):
+            new_yerr = np.append(new_yerr, 0)
+        else:
+            new_yerr = np.append(new_yerr, std_dev)
+        w_i = w_i + 1
+    return new_xdata, new_ydata, new_yerr
+
 
 def get_exponent(value):
     return np.floor(np.log10(np.abs(value))).astype(int)

ada/gui/load_window.py

@@ -56,9 +56,10 @@ def initUI(self):
 
         # Dropdown list of available file types
         if self.row == -1:
-            self.file_type = DropDown('File type:', config.replicate_types, self)
-        else:
             self.file_type = DropDown('File type:', config.file_types, self)
+        else:
+            self.file_type = DropDown('File type:', config.replicate_types, self)
+        self.file_type.entry.currentTextChanged.connect(self.update_options)
         layout.addWidget(self.file_type)
 
         # Button for selecting files to import
@@ -134,7 +135,7 @@ def update_options(self):
             self.details_file_list.show()
             self.merge_replicates.show()
         # Allow condition files to be added if not dealing with replicates
-        if (file_type == 'Algem HT24' or file_type == 'Algem Pro') and self.row == -1:
+        if file_type == 'Algem HT24' or file_type == 'Algem Pro':
             self.select_conditions_button.show()
             self.conditions_file_list.show()
             self.downsample.show()
@@ -190,6 +191,16 @@ def load_algem_pro(self, file_name):
         else:
             data_manager.growth_data.add_replicate(algem_data, self.row)
 
+    def load_algem_pro_conditions(self, file_name, downsample):
+        logger.info('Loading Algem-Pro condition file %s, downsample %i' %
+                    (file_name, downsample))
+        # Read in conditions files from Algem Pro
+        algem_conditions = read_algem_pro(file_name, downsample)
+        if self.row == -1:
+            data_manager.condition_data.add_data(algem_conditions)
+        else:
+            data_manager.condition_data.add_replicate(algem_conditions, self.row)
+
     def load_algem_ht24_txt(self, file_name):
         downsample = self.downsample.get_int()
 
@@ -232,6 +243,30 @@ def load_algem_ht24(self, file_name):
                 else:
                     data_manager.growth_data.add_data(replicate[0])
 
+    def load_algem_ht24_conditions(self, file_name, downsample):
+        logger.info('Loading HT-24 condition file %s, downsample %i' %
+                    (file_name, downsample))
+        # Read in files from Algem HT24 if details file is provided
+        if len(self.details) == 0:
+            algem_conditions_list = read_algem_ht24(file_name,
+                                                    downsample)
+            for algem_conditions in algem_conditions_list:
+                data_manager.condition_data.add_data(algem_conditions)
+
+        # Read in files from Algem HT24 without details file
+        else:
+            algem_conditions_list, replicate_conditions_list = \
+                read_algem_ht24_details(file_name, self.details[0],
+                                        downsample)
+            for algem_conditions in algem_conditions_list:
+                data_manager.condition_data.add_data(algem_conditions)
+            for replicate in replicate_conditions_list:
+                if self.merge_replicates.isChecked():
+                    data_manager.condition_data.add_replicate(replicate[0],
+                                                 replicate[1])
+                else:
+                    data_manager.condition_data.add_data(replicate[0])
+
     def load_ip(self, file_name):
         logger.info('Loading IP file %s' % file_name)
         # Read in files from Industrial Plankton
@@ -245,6 +280,7 @@ def load_ip(self, file_name):
             data_manager.condition_data.add_data(condition_data)
         else:
             data_manager.growth_data.add_replicate(ip_data, self.row)
+            data_manager.condition_data.add_replicate(condition_data, self.row)
 
     def load_psi(self, file_name):
         logger.info('Loading PSI file %s' % file_name)
@@ -259,6 +295,7 @@ def load_psi(self, file_name):
             data_manager.condition_data.add_data(condition_data)
         else:
             data_manager.growth_data.add_replicate(psi_data, self.row)
+            data_manager.condition_data.add_replicate(condition_data, self.row)
 
     def load_ada(self, file_name):
         logger.info('Loading ADA file %s' % file_name)
@@ -269,37 +306,8 @@ def load_ada(self, file_name):
                 data_manager.condition_data.add_data(condition_data)
         else:
             data_manager.growth_data.add_replicate(ada_data, self.row)
-
-    def load_algem_pro_conditions(self, file_name, downsample):
-        logger.info('Loading Algem-Pro condition file %s, downsample %i' %
-                    (file_name, downsample))
-        # Read in conditions files from Algem Pro
-        algem_conditions = read_algem_pro(file_name, downsample)
-        data_manager.condition_data.add_data(algem_conditions)
-
-    def load_algem_ht24_conditions(self, file_name, downsample):
-        logger.info('Loading HT-24 condition file %s, downsample %i' %
-                    (file_name, downsample))
-        # Read in files from Algem HT24 if details file is provided
-        if len(self.details) == 0:
-            algem_conditions_list = read_algem_ht24(file_name,
-                                                    downsample)
-            for algem_conditions in algem_conditions_list:
-                data_manager.condition_data.add_data(algem_conditions)
-
-        # Read in files from Algem HT24 without details file
-        else:
-            algem_conditions_list, replicate_conditions_list = \
-                read_algem_ht24_details(file_name, self.details[0],
-                                        downsample)
-            for algem_conditions in algem_conditions_list:
-                data_manager.condition_data.add_data(algem_conditions)
-            for replicate in replicate_conditions_list:
-                if self.merge_replicates.isChecked():
-                    data_manager.condition_data.add_replicate(replicate[0],
-                                                 replicate[1])
-                else:
-                    data_manager.condition_data.add_data(replicate[0])
+            if condition_data is not None:
+                data_manager.condition_data.add_replicate(condition_data, self.row)
 
     @error_wrapper
     def load(self):