fixes to plotting functions

ccpem · Jun 27, 2024 · 11b542b · 11b542b
1 parent 37a9685
commit 11b542b
Show file tree

Hide file tree

Showing 4 changed files with 39 additions and 16 deletions.
diff --git a/src/roodmus/analysis/plot_alignment.py b/src/roodmus/analysis/plot_alignment.py
@@ -178,7 +178,7 @@ def true_pose_distribution_plot(
         cmap="RdYlBu_r",
         marginal_kws=dict(bins=100, fill=False),
     )
-    grid.fig.set_size_inches(14, 7)
+    grid.figure.set_size_inches(7, 3.5)
     # adjust the x and y ticks to show multiples of pi
     grid.ax_joint.set_xticks(
         [
@@ -204,7 +204,8 @@ def true_pose_distribution_plot(
             "\u03C0/2",
             "3/4\u03C0",
             "\u03C0",
-        ]
+        ],
+        rotation=45,
     )
     grid.ax_joint.set_yticks([0, np.pi / 4, np.pi / 2, 3 / 4 * np.pi, np.pi])
     grid.ax_joint.set_yticklabels(
@@ -215,7 +216,9 @@ def true_pose_distribution_plot(
     # add new sublot to the right of the jointplot
     cbar_ax = grid.fig.add_axes([1, 0.15, 0.02, 0.7])
     # add colorbar to the new subplot
-    grid.fig.colorbar(grid.ax_joint.collections[0], cax=cbar_ax, label="count")
+    grid.figure.colorbar(
+        grid.ax_joint.collections[0], cax=cbar_ax, label="Count"
+    )
     if vmin and vmax:
         # set limits of the colorbar to the same as for
         # the picked particles
@@ -224,7 +227,7 @@ def true_pose_distribution_plot(
         # get the limits of the colorbar
         vmin, vmax = grid.ax_joint.collections[0].get_clim()
     # add title to the top of the jointplot
-    grid.fig.suptitle("true particle pose distribution", fontsize=20, y=1.05)
+    grid.fig.suptitle("Ground-Truth pose distribution", fontsize=21, y=1.05)
 
     return grid, vmin, vmax
 
@@ -351,7 +354,7 @@ def picked_pose_distribution_plot(
         cmap="RdYlBu_r",
         marginal_kws=dict(bins=100, fill=False),
     )
-    grid.fig.set_size_inches(14, 7)
+    grid.fig.set_size_inches(7, 3.5)
     # adjust the x and y ticks to show multiples of pi
     grid.ax_joint.set_xticks(
         [
@@ -377,7 +380,8 @@ def picked_pose_distribution_plot(
             "\u03C0/2",
             "3/4\u03C0",
             "\u03C0",
-        ]
+        ],
+        rotation=45,
     )
     grid.ax_joint.set_yticks([0, np.pi / 4, np.pi / 2, 3 / 4 * np.pi, np.pi])
     grid.ax_joint.set_yticklabels(
@@ -386,9 +390,11 @@ def picked_pose_distribution_plot(
     grid.ax_joint.set_xlabel("Azimuth")
     grid.ax_joint.set_ylabel("Tilt")
     # add new sublot to the right of the jointplot
-    cbar_ax = grid.fig.add_axes([1, 0.15, 0.02, 0.7])
+    cbar_ax = grid.figure.add_axes([1, 0.15, 0.02, 0.7])
     # add colorbar to the new subplot
-    grid.fig.colorbar(grid.ax_joint.collections[0], cax=cbar_ax, label="count")
+    grid.figure.colorbar(
+        grid.ax_joint.collections[0], cax=cbar_ax, label="Count"
+    )
     if vmin and vmax:
         # set limits of the colorbar to the
         # same as for the picked particles
@@ -397,7 +403,9 @@ def picked_pose_distribution_plot(
         # get the limits of the colorbar
         vmin, vmax = grid.ax_joint.collections[0].get_clim()
     # add title to the top of the jointplot
-    grid.fig.suptitle("picked particle pose distribution", fontsize=20, y=1.05)
+    grid.figure.suptitle(
+        "Picked particle pose distribution", fontsize=21, y=1.05
+    )
 
     return grid, vmin, vmax
 

diff --git a/src/roodmus/analysis/plot_ctf.py b/src/roodmus/analysis/plot_ctf.py
@@ -408,8 +408,8 @@ def plot_defocus_scatter(
     ax[0].set_xlabel("defocus truth [$\u212B$]")
     ax[1].set_xlabel("defocus truth [$\u212B$]")
     ax[0].set_ylabel("defocusU estimated [$\u212B$]")
-    ax[0].set_title("defocusU")
-    ax[1].set_title("defocusV")
+    ax[0].set_title("DefocusU (\u03bcm)")
+    ax[1].set_title("DefocusV (\u03bcm)")
     ax[0].grid(False)
     ax[1].grid(False)
     # add colorbar legend
@@ -421,7 +421,7 @@ def plot_defocus_scatter(
     )
     sm._A = []
     cbar = plt.colorbar(sm)
-    cbar.set_label("micrograph")
+    cbar.set_label("Micrograph")
     fig.tight_layout()
     return fig, ax
 

diff --git a/src/roodmus/analysis/plot_picking.py b/src/roodmus/analysis/plot_picking.py
@@ -2221,7 +2221,9 @@ def plot_precision(
     )
     sm._A = []
     cbar = fig.colorbar(sm, ax=ax)
-    cbar.set_label("defocus (\u03bcm)", rotation=270, labelpad=20, fontsize=12)
+    cbar.set_label("Defocus (\u03bcm)", rotation=270, labelpad=20, fontsize=21)
+    # change tick labels of the colourbar to use 18 fontsize
+    cbar.ax.tick_params(labelsize=18)
     # add labels
     ax.set_xlabel("")
     ax.set_ylabel("precision", fontsize=14)
@@ -2289,7 +2291,8 @@ def plot_recall(
     )
     sm._A = []
     cbar = fig.colorbar(sm, ax=ax)
-    cbar.set_label("defocus (\u03bcm)", rotation=270, labelpad=20, fontsize=12)
+    cbar.set_label("Defocus (\u03bcm)", rotation=270, labelpad=20, fontsize=21)
+    cbar.ax.tick_params(labelsize=18)
     # add labels
     ax.set_xlabel("")
     ax.set_ylabel("recall", fontsize=14)

diff --git a/src/roodmus/analysis/utils.py b/src/roodmus/analysis/utils.py
@@ -1529,7 +1529,7 @@ def _match_particles(
         results_truth: pd.DataFrame,
         verbose: bool = False,
         enable_tqdm: bool = False,
-    ) -> Tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame, pd.DataFrame,]:
+    ) -> Tuple:
         """When picked and truth dfs are loaded, this can be used to create
         dataframes of matched picked particles, matched truth particles,
         picked particles not matched to truth particles and finally, truth
@@ -1580,6 +1580,9 @@ def _match_particles(
         matched_truth_dfs = []
         unmatched_picked_dfs = []
         unmatched_truth_dfs = []
+        # list to hold all indices of matched truth particles
+        # for the total number of picked particles
+        truth_index_for_picked = []
 
         # loop over the metadata files
         if isinstance(metadata_filenames, str):
@@ -1653,6 +1656,7 @@ def _match_particles(
                             )
                         # no particle is matched to picked particle
                         # and we move on to next particle
+                        truth_index_for_picked.append(np.nan)
                         continue
                     # check if closest truth particle is within particle
                     # diameter of picked particle
@@ -1661,6 +1665,7 @@ def _match_particles(
                         > self.particle_diameter
                     ):
                         closest_truth_index.append(np.nan)
+                        truth_index_for_picked.append(np.nan)
                         continue
                     # if it is, consider picking successful and allow the
                     # pickedand truth particle to be associated with each
@@ -1672,6 +1677,12 @@ def _match_particles(
                         p_match.append(j)
                         t_match.append(truth_particle_index)
 
+                        # to the list of truth indices for picked particles
+                        # add the index of the truth particle in results_truth
+                        truth_index_for_picked.append(
+                            ugraph_truth.index[truth_particle_index]
+                        )
+
                 # check whether any truth particles had multiple
                 # picked particles mapped to them
                 non_unique_count = len(
@@ -1697,7 +1708,7 @@ def _match_particles(
                             ugraph,
                         )
                     )
-                if non_unique_count > 0:
+                if non_unique_count > 0 and verbose:
                     print(
                         "This may cause problems with overwritten assns"
                         " in truth particles dict!"
@@ -1775,6 +1786,7 @@ def _match_particles(
             matched_truth_df,
             unmatched_picked_df,
             unmatched_truth_df,
+            truth_index_for_picked,
         )
 
     def _calc_neighbours(self, pos_picked, pos_truth, r):