Add new module logging_utils and update main modules to use it.

Author: NikoOinonen

ppafm/GUIWidgets.py

@@ -8,6 +8,10 @@
 from PyQt5 import QtCore, QtWidgets
 
 from . import io
+from .logging_utils import get_logger, get_perf_logger
+
+logger = get_logger("GUIWidgets")
+perf_logger = get_perf_logger("GUIWidgets")
 
 matplotlib.use("Qt5Agg")
 
@@ -129,8 +133,7 @@ def __init__(self, parentWiget=None, parentApp=None, width=5, height=4, dpi=100,
     def plotSlice(self, F_stack, z_slice, title=None, margins=None, grid_selector=0, slice_length=None, points=[], cbar_range=None, extent=None):
         F = F_stack[z_slice]
 
-        if self.verbose > 0:
-            print("plotSlice F.shape, F.min(), F.max(), margins", F.shape, F.min(), F.max(), margins)
+        logger.debug(f"plotSlice F.shape, F.min(), F.max(), margins {F.shape} {F.min()} {F.max()} {margins}")
 
         if self.img is None or self.img.get_array().shape != F.shape:
             self.axes.cla()
@@ -143,8 +146,7 @@ def plotSlice(self, F_stack, z_slice, title=None, margins=None, grid_selector=0,
                 for line in self.axes.lines:
                     line.remove()
                 self.axes.set_prop_cycle(None)  # Reset color cycle
-                if self.verbose > 0:
-                    print("plotSlice: reset points")
+                logger.debug("plotSlice: reset points")
             else:
                 for p, (ix, iy) in zip(self.axes.lines, points):
                     x = np.atleast_1d(ix)
@@ -155,17 +157,15 @@ def plotSlice(self, F_stack, z_slice, title=None, margins=None, grid_selector=0,
             if self.cbar == None:
                 self.cbar = self.fig.colorbar(self.img, ax=self.axes)
                 self.cbar.set_label("df (Hz)")
-                if self.verbose > 0:
-                    print("plotSlice: added colorbar")
+                logger.debug("plotSlice: added colorbar")
             self.img.set_clim(vmin=cbar_range[0], vmax=cbar_range[1])
             self.cbar.mappable.set_clim(vmin=cbar_range[0], vmax=cbar_range[1])
         else:
             self.img.autoscale()
             if self.cbar is not None:
                 self.cbar.remove()
                 self.cbar = None
-                if self.verbose > 0:
-                    print("plotSlice: removed colorbar")
+                logger.debug("plotSlice: removed colorbar")
 
         if extent is not None:
             self.img.set_extent(extent)
@@ -197,9 +197,9 @@ def plotSlice2(self, F_stack, title=None, margins=None, grid_selector=0, slice_l
         self.axes.cla()
 
         F = F_stack
-        print("plotSlice F.shape, F.min(), F.max() ", F.shape, F.min(), F.max())
+        logger.debug(f"plotSlice F.shape, F.min(), F.max() {F.shape} {F.min()} {F.max()}")
 
-        print("self.margins", margins)
+        logger.debug(f"self.margins {margins}")
         if alpha > 0 and big_len_image is not None:
             F = F * (1 - alpha) + big_len_image * alpha
         self.img = self.axes.imshow(F, origin="lower", cmap="viridis", interpolation="bicubic")
@@ -232,8 +232,7 @@ def onclick(self, event):
             x = float(event.xdata)
             y = float(event.ydata)
         except TypeError:
-            if self.verbose > 0:
-                print("Invalid click event.")
+            logger.warning("Invalid click event.")
             return
         self.axes.plot([x], [y], "o", scalex=False, scaley=False)
         self.draw()
@@ -247,15 +246,14 @@ def onscroll(self, event):
             x = float(event.xdata)
             y = float(event.ydata)
         except TypeError:
-            if self.verbose > 0:
-                print("Invalid scroll event.")
+            logger.warning("Invalid scroll event.")
             return
         if event.button == "up":
             direction = "in"
         elif event.button == "down":
             direction = "out"
         else:
-            print(f"Invalid scroll direction {event.button}")
+            logger.warning(f"Invalid scroll direction {event.button}")
             return
         self.parent.zoomTowards(x, y, direction)
 
@@ -325,7 +323,7 @@ def save_dat(self):
         fileName, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save df curve raw data", default_path, "Data files (*.dat)")
         if fileName:
             fileName = correct_ext(fileName, ".dat")
-            print("saving data to :", fileName)
+            logger.info(f"Saving data to: {fileName}")
             data = []
             data.append(np.array(self.figCan.axes.lines[0].get_xdata()))
             for line in self.figCan.axes.lines:
@@ -338,7 +336,7 @@ def save_png(self):
         fileName, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save df curve image", default_path, "Image files (*.png)")
         if fileName:
             fileName = correct_ext(fileName, ".png")
-            print("saving image to :", fileName)
+            logger.info(f"Saving image to: {fileName}")
             self.figCan.fig.savefig(fileName, bbox_inches="tight")
 
     def clearFig(self):
@@ -363,7 +361,7 @@ def setRange(self):
         except:
             pass
         self.figCan.draw()
-        print("range: ", xmin, xmax, ymin, ymax)
+        logger.debug(f"range: {xmin} {xmax} {ymin} {ymax}")
 
 
 # =======================
@@ -576,8 +574,7 @@ def updateFF(self):
         if not self.isVisible():
             set_widget_value(self.bxInd, iz)
 
-        if self.verbose > 0:
-            print("FFViewer.updateFF", self.FE.shape, iz, self.z_step, self.z_min)
+        logger.debug(f"FFViewer.updateFF {self.FE.shape} {iz} {self.z_step} {self.z_min}")
 
     def updateView(self):
         t0 = time.perf_counter()
@@ -588,10 +585,8 @@ def updateView(self):
         data = self.FE[..., ic].transpose(2, 1, 0)
         self.figCan.plotSlice(data, iz, title=f"z = {z:.2f}Å")
 
-        if self.verbose > 0:
-            print("FFViewer.updateView", ic, iz, data.shape)
-        if self.verbose > 1:
-            print("updateView time [s]", time.perf_counter() - t0)
+        logger.debug(f"FFViewer.updateView {ic} {iz} {data.shape}")
+        perf_logger.info(f"updateView time [s] {time.perf_counter() - t0}")
 
     def saveFF(self):
         comp = self.slComponent.currentText()
@@ -602,12 +597,11 @@ def saveFF(self):
         ext = os.path.splitext(fileName)[1]
         if ext != ".xsf":
             self.parent.status_message("Unsupported file type in force field save file path")
-            print(f"Unsupported file type in force field save file path `{fileName}`")
+            logger.error(f"Unsupported file type in force field save file path `{fileName}`")
             return
         self.parent.status_message("Saving data...")
 
-        if self.verbose > 0:
-            print(f"Saving force field data to {fileName}...")
+        logger.debug(f"Saving force field data to {fileName}...")
         ic = self.slComponent.currentIndex()
         data = self.FE.copy()
         # Clamp large values for easier visualization
@@ -620,10 +614,9 @@ def saveFF(self):
         lvec = self.parent.afmulator.lvec
         xyzs = self.parent.xyzs - lvec[0]
         atomstring = io.primcoords2Xsf(self.parent.Zs, xyzs.T, lvec)
-        io.saveXSF(fileName, data, lvec, head=atomstring, verbose=0)
+        io.saveXSF(fileName, data, lvec, head=atomstring)
 
-        if self.verbose > 0:
-            print("Done saving force field data.")
+        logger.info("Done saving force field data.")
         self.parent.status_message("Ready")
 
 

ppafm/GridUtils.py

@@ -5,6 +5,9 @@
 import numpy as np
 
 from . import cpp_utils
+from .logging_utils import get_logger
+
+logger = get_logger("GridUtils")
 
 # ============================== interface to C++ core
 
@@ -97,7 +100,7 @@ def interpolate_cartesian(F, pos, cell=None, result=None):
     if cell is not None:
         setGridCell(cell)
     nDim = np.array(pos.shape)
-    print(nDim)
+    logger.debug(nDim)
     if result is None:
         result = np.zeros((nDim[0], nDim[1], nDim[2]))
     n = nDim[0] * nDim[1] * nDim[2]
@@ -120,9 +123,9 @@ def dens2Q_CHGCARxsf(data, lvec):
     nDim = data.shape
     Ntot = nDim[0] * nDim[1] * nDim[2]
     Vtot = np.linalg.det(lvec[1:])
-    print("dens2Q Volume    : ", Vtot)
-    print("dens2Q Ntot      : ", Ntot)
-    print("dens2Q Vtot/Ntot : ", Vtot / Ntot)
+    logger.debug(f"dens2Q Volume    : {Vtot}")
+    logger.debug(f"dens2Q Ntot      : {Ntot}")
+    logger.debug(f"dens2Q Vtot/Ntot : {Vtot / Ntot}")
     # Qsum = rho1.sum()
     return Vtot / Ntot