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-rw-r--r--libcrystfel/src/cell-utils.c3
-rw-r--r--libcrystfel/src/cell.c4
-rw-r--r--libcrystfel/src/image-cbf.c3
-rw-r--r--libcrystfel/src/image-hdf5.c2
-rw-r--r--libcrystfel/src/image.c4
-rw-r--r--libcrystfel/src/indexers/mosflm.c28
-rw-r--r--libcrystfel/src/indexers/taketwo.c2
-rw-r--r--libcrystfel/src/integration.c2
-rw-r--r--libcrystfel/src/predict-refine.c2
-rw-r--r--libcrystfel/src/reflist-utils.c2
-rw-r--r--libcrystfel/src/stream.c1
-rw-r--r--scripts/plot-cc-and-scale.R2
-rw-r--r--src/crystfel_gui.c2
-rw-r--r--src/crystfelimageview.c2
-rw-r--r--src/geoptimiser.c6
15 files changed, 15 insertions, 50 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 31ba9d35..30744bd4 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1332,8 +1332,7 @@ double lowest_reflection(UnitCell *cell)
signed int h, k, l;
double lowres = INFINITY;
- /* FIXME: Inelegant and nasty. Anyone want to work out
- * all the possible cases? */
+ /* Boring brute-force approach */
for ( h=0; h<4; h++ ) {
for ( k=0; k<4; k++ ) {
for ( l=0; l<4; l++ ) {
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 4dea2ce1..775567e3 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -884,7 +884,7 @@ UnitCell *cell_transform_rational(UnitCell *cell, RationalMatrix *m)
ncen = determine_centering(m, cell_get_centering(cell));
cell_set_centering(out, ncen);
- /* FIXME: Update unique axis, lattice type */
+ /* FIXME: Update unique axis, lattice type (GitLab #39) */
cell_set_lattice_type(out, L_TRICLINIC);
cell_set_unique_axis(out, '?');
@@ -972,7 +972,7 @@ UnitCell *cell_transform_rational_inverse(UnitCell *cell, RationalMatrix *m)
out = cell_transform_gsl_direct(cell, inv);
- /* FIXME: Update centering, unique axis, lattice type */
+ /* FIXME: Update centering, unique axis, lattice type (GitLab #39) */
gsl_matrix_free(tm);
gsl_matrix_free(inv);
diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
index 19b38607..859ef731 100644
--- a/libcrystfel/src/image-cbf.c
+++ b/libcrystfel/src/image-cbf.c
@@ -635,8 +635,7 @@ int image_cbf_read(struct image *image,
int image_cbf_read_header_to_cache(struct image *image,
const char *from)
{
- /* FIXME: Implementation
- * https://gitlab.desy.de/thomas.white/crystfel/-/issues/10 */
+ /* FIXME: Implementation (GitLab #10) */
ERROR("Reading headers from CBF files is not currently supported.\n");
return 1;
}
diff --git a/libcrystfel/src/image-hdf5.c b/libcrystfel/src/image-hdf5.c
index 2995654d..497ce763 100644
--- a/libcrystfel/src/image-hdf5.c
+++ b/libcrystfel/src/image-hdf5.c
@@ -685,7 +685,7 @@ int image_hdf5_read_header_to_cache(struct image *image, const char *name)
type = H5Dget_type(dh);
class = H5Tget_class(type);
- /* FIXME: Handle strings as well */
+ /* FIXME: Handle strings as well (GitLab #36) */
if ( (class != H5T_FLOAT) && (class != H5T_INTEGER) ) {
ERROR("Not a floating point or integer value.\n");
close_hdf5(fh);
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 10313ca8..7ec79eaf 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -462,7 +462,7 @@ static double get_value(struct image *image, const char *from,
if ( image_read_header_float(image, from, &val) == 0 ) {
return val;
} else {
- return NAN; /* FIXME: Use out-of-band flag */
+ return NAN; /* FIXME: Use out-of-band flag (GitLab #37) */
}
}
@@ -767,10 +767,8 @@ static void set_image_parameters(struct image *image,
image->bw = dtempl->bandwidth;
- /* FIXME: Possibly load spectrum from file */
image->spectrum = spectrum_generate_gaussian(image->lambda,
image->bw);
-
}
diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c
index 02532103..c56f3ae6 100644
--- a/libcrystfel/src/indexers/mosflm.c
+++ b/libcrystfel/src/indexers/mosflm.c
@@ -29,31 +29,6 @@
*
*/
-/* TODO:
- *
- * Properly read the newmat file (don't use fscanf-- spaces between numers
- * are not guaranteed)
- *
- * "Success" is indicated by existence of NEWMAT file written by mosflm.
- * Better to interact with mosflm directly in order to somehow verify success.
- *
- * Investigate how these keywords affect mosflms behavior:
- *
- * MOSAICITY
- * DISPERSION
- * DIVERGENCE
- * POLARISATION
- * POSTREF BEAM
- * POSTREF USEBEAM OFF
- * PREREFINE ON
- * EXTRA ON
- * POSTREF ON
- *
- * These did not seem to affect the results by my (Rick's) experience, probably
- * because they are only used conjunction with image intensity data, but it's
- * worth another look at the documentation.
- */
-
#include <libcrystfel-config.h>
#include <stdlib.h>
@@ -575,8 +550,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
&a, &b, &c, &alpha, &beta, &gamma);
cen = cell_get_centering(mosflm->mp->template);
/* Old MOSFLM simply ignores CELL and CENTERING subkeywords.
- * So this doesn't do any harm.
- * TODO: but still better to show WARNING if MOSFLM is old. */
+ * So this doesn't do any harm. */
snprintf(tmp, 255, "AUTOINDEX DPS FILE %s IMAGE 1 "
"MAXCELL 1000 REFINE "
"CELL %.1f %.1f %.1f %.1f %.1f %.1f "
diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c
index 4b481e93..8ce33083 100644
--- a/libcrystfel/src/indexers/taketwo.c
+++ b/libcrystfel/src/indexers/taketwo.c
@@ -248,8 +248,6 @@ struct TakeTwoCell
/* Final required step size for refinement of solutions */
#define ANGLE_CONVERGE_SIZE (deg2rad(0.01))
-/* TODO: Multiple lattices */
-
/* ------------------------------------------------------------------------
* apologetic function
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 45f5f677..b2b6ccfa 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -355,7 +355,7 @@ static void fit_gradient_bg(struct intcontext *ic, struct peak_box *bx)
}
}
- /* FIXME: SVD is massive overkill here */
+ /* SVD is massive overkill here, but the routine is right there. */
ans = solve_svd(v, bx->bgm, NULL, 0);
gsl_vector_free(v);
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index b871f43a..9b562fb0 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -257,7 +257,7 @@ static int pair_peaks(struct image *image, Crystal *cr,
get_detector_pos(refl, &fs, &ss);
pd = pow(fs - rps[i].peak->fs, 2.0)
+ pow(ss - rps[i].peak->ss, 2.0);
- if ( pd > 10.0 * 10.0 ) continue; /* FIXME Hardcoded distance */
+ if ( pd > 10.0 * 10.0 ) continue; /* FIXME Hardcoded distance (GitLab #38) */
rps[n_acc] = rps[i];
rps[n_acc].refl = reflection_new(h, k, l);
diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index c354cb19..2b250eff 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -1077,7 +1077,7 @@ int write_to_mtz(RefList *reflist,
cellp[4] = rad2deg(be);
cellp[5] = rad2deg(ga);
- /* FIXME: Proposed labelling:
+ /* FIXME: Proposed labelling (GitLab #28):
* title = as above
* project = basename of folder containing crystfel.project
* crystal = name of indexing results run
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 47438614..ba6e13c8 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -1082,7 +1082,6 @@ struct image *stream_read_chunk(Stream *st, StreamFlags srf)
image_set_zero_data(image, st->dtempl_read);
image_set_zero_mask(image, st->dtempl_read);
}
- /* FIXME: Maybe arbitrary spectrum from file (?) */
image->spectrum = spectrum_generate_gaussian(image->lambda,
image->bw);
return image;
diff --git a/scripts/plot-cc-and-scale.R b/scripts/plot-cc-and-scale.R
index b67ab058..97c643d3 100644
--- a/scripts/plot-cc-and-scale.R
+++ b/scripts/plot-cc-and-scale.R
@@ -5,8 +5,6 @@
scale_cc <- read.table("stats.dat", col.names=c("ImageName", "ScaleFactor", "CC"))
# scatter plot
-# FIXME: sometimes white lines appear on the plot.
-# seems to be a bug in smoothScatter
smoothScatter(scale_cc$ScaleFactor, scale_cc$CC,
nbin=200, xlim=c(0, 2), ylim=c(0, 1),
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index 28661064..700cc4f1 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -640,7 +640,7 @@ static void add_button(GtkWidget *vbox, const char *label, const char *imagen,
static void add_task_buttons(GtkWidget *vbox, struct crystfelproject *proj)
{
- /* FIXME: All these icons are placeholders */
+ /* FIXME: All these icons are placeholders (GitLab #9) */
add_button(vbox, "Load data", "folder-pictures",
G_CALLBACK(import_sig), proj);
add_button(vbox, "Peak detection", "edit-find",
diff --git a/src/crystfelimageview.c b/src/crystfelimageview.c
index 8302ae44..12ef1dee 100644
--- a/src/crystfelimageview.c
+++ b/src/crystfelimageview.c
@@ -239,7 +239,7 @@ static void draw_pixel_values(cairo_t *cr,
PangoFontDescription *fontdesc;
double w, h;
- /* FIXME: This is wrong for slanty pixels */
+ /* FIXME: This is wrong for slanty pixels (GitLab #17) */
min_fs = clamp(imin_fs, 0, p.w-1);
min_ss = clamp(imin_ss, 0, p.h-1);
max_fs = clamp(imax_fs, 0, p.w-1);
diff --git a/src/geoptimiser.c b/src/geoptimiser.c
index 24a159de..f28e9551 100644
--- a/src/geoptimiser.c
+++ b/src/geoptimiser.c
@@ -1074,7 +1074,7 @@ static DataTemplate *correct_rotation_and_stretch(struct rg_collection *connecte
struct geoptimiser_params *gparams)
{
#if 0
- /* FIXME ! */
+ /* FIXME (GitLab #29) */
int di, ip;
STATUS("Applying rotation and stretch corrections.\n");
@@ -1392,7 +1392,7 @@ static void correct_shift(struct rg_collection *connected,
double clen_to_use)
{
#if 0
- /* FIXME ! */
+ /* FIXME (GitLab #29) */
int di;
int ip;
@@ -1585,7 +1585,7 @@ static double compute_rotation_and_stretch(struct rg_collection *connected,
num_pix_first_p = first_p->w * first_p->h;
- /* FIXME: minrad here is not universal */
+ /* FIXME: minrad here is not universal (GitLab #29) */
min_dist = dist_coeff_for_rot_str * sqrt(num_pix_first_p
* connected->rigid_groups[di]->n_panels);
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-20 14:27:07 +0000