Package: release.debian.org Severity: normal User: release.debian....@packages.debian.org Usertags: unblock
Please unblock package yorick-mira Dear release team, This upload fixes #856835 (important): ymira crashes when trying to fit several wavelengths https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=856835 Due to this bugs, users of multi-wavelength interferometric instruments cannot use the high-level wrapper `ymira' to reconstruct images from their interferometric measuremetns, but need to know enough of the Yorick language to load their data into a Yorick interactive session launch the image reconstruction from there. In other words, this bug is not RC but has a serious impact on the usability of the package for most users. The fix is backported from upstream's latest release (1.1.1). A source debdiff is attached. Kind regards, Thibaut. unblock yorick-mira/1.1.0+git20170124.3bd1c3~dfsg1-2 -- System Information: Debian Release: 9.0 APT prefers testing APT policy: (900, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.9.0-1-amd64 (SMP w/8 CPU cores) Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8)
diff -Nru yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/changelog yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/changelog --- yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/changelog 2017-01-25 12:30:39.000000000 +0100 +++ yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/changelog 2017-03-05 11:43:23.000000000 +0100 @@ -1,3 +1,10 @@ +yorick-mira (1.1.0+git20170124.3bd1c3~dfsg1-2) unstable; urgency=low + + * Bug fix: "ymira crashes when trying to fit several wavelengths" + (Closes: #856835). + + -- Thibaut Paumard <thib...@debian.org> Sun, 05 Mar 2017 11:43:23 +0100 + yorick-mira (1.1.0+git20170124.3bd1c3~dfsg1-1) unstable; urgency=low * New upstream version 1.1.0+git20170124.3bd1c3~dfsg1 diff -Nru yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/monochromatic-doesnt-work yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/monochromatic-doesnt-work --- yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/monochromatic-doesnt-work 1970-01-01 01:00:00.000000000 +0100 +++ yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/monochromatic-doesnt-work 2017-03-05 11:42:15.000000000 +0100 @@ -0,0 +1,267 @@ +Description: ymira crashes when using several wavelengths +Origin: upstream +Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=856835 +Applied-Upstream: c0a8a9c73d6a032979e9c96cb93bf78d5d9f6cea +Reviewed-by: Thibaut Paumard <thib...@debian.org> +Last-Update: 2017-03-05 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/src/mira-batch.i ++++ b/src/mira-batch.i +@@ -193,7 +193,6 @@ + /* Constants and shortcuts. */ + FALSE = 0n; + TRUE = 1n; +- monochromatic = TRUE; + format = mira_format; + + opt = opt_parse(_MIRA_OPTIONS, argv); +@@ -350,13 +349,11 @@ + naxis2 = img.naxis2; + naxis3 = (naxis >= 3 ? img.naxis3 : 1); + eq_nocopy, initial, img.arr; +- if (monochromatic) { +- if (naxis == 3) { ++ if (naxis == 3) { + if (naxis3 != 1) { + opt_error, "expecting a 2D initial image"; + } + initial = initial(,,avg); +- } + } + // FIXME: only the pixel size is considered... + +@@ -427,7 +424,6 @@ + eff_band = opt.effband, + wavemin = opt.wavemin, + wavemax = opt.wavemax, +- monochromatic = monochromatic, + quiet = opt.quiet); + + mira_config, master, dim=dim, pixelsize=pixelsize, xform=opt.xform; +--- a/src/mira.i ++++ b/src/mira.i +@@ -289,8 +289,6 @@ + * MASTER.vis - complex visibility data (see below for layout) + * MASTER.vis2 - powerspectrum data (see below for layout) + * MASTER.vis3 - bispectrum data (see below for layout) +- * MASTER.monochromatic - monochromatic or gray case? +- * MASTER.monochromatic_option - monochromatic option as set by user + * MASTER.u - list of measured spatial frequencies + * MASTER.v - list of measured spatial frequencies + * MASTER.w - list of measured wavelenghts +@@ -375,7 +373,7 @@ + * + * DB.u ~ MASTER.u(DB.idx)*DB.sgn + * DB.v ~ MASTER.v(DB.idx)*DB.sgn +- * DB.w ~ MASTER.w(DB.idx) // not in monochromatic mode ++ * DB.w ~ MASTER.w(DB.idx) + * + * where MASTER is the parent of datablock DB + * +@@ -383,7 +381,7 @@ + + func mira_new(.., wavemin=, wavemax=, + eff_wave=, eff_band=, wave_tol=, +- quiet=, base_tol=, monochromatic=, ++ quiet=, base_tol=, + noise_method=, noise_level=, + cleanup_bad_data=, target=, goodman=, + no_t3=, no_vis=, no_vis2=) +@@ -401,6 +399,10 @@ + EFF_BAND = Effective spectral bandwidth (units: meters), default value + is 1e-7 (0.1 micron). + ++ WAVEMIN = Lower bound for the selected wavelength range (in meters). ++ ++ WAVEMAX = Upper bound for the selected wavelength range (in meters). ++ + WAVE_TOL = Tolerance for wavelength grouping (units: meters). Default + value is 1e-10 (1 Ångström). This tolerance is used to decide + whether different wavelengths correspond to the same one. +@@ -409,9 +411,6 @@ + value is 1e-3 (1 millimeter). This tolerance is used to decide + whether different positions correspond to the same baseline. + +- MONOCHROMATIC = True if a monochromatic (gray) model of the object +- brightness distribution is to be reconstructed. +- + NO_VIS = True to not use complex visibilities (OI_VIS data-blocks). + + NO_VIS2 = True to not use powerspectrum data (OI_VIS2 data-blocks). +@@ -460,7 +459,6 @@ + */ + { + if (is_void(quiet)) quiet = 0; +- if (is_void(monochromatic)) monochromatic = 1n; + + /* Get spectral bandwidth parameters (in meters). */ + choice = ((is_void(wavemin) ? 0 : 1) | +@@ -511,7 +509,6 @@ + eff_band = eff_band, + wave_tol = wave_tol, + base_tol = base_tol, +- monochromatic_option = monochromatic, + flags = 0, + flux_weight = 0.0, + flux_mean = 1.0, +@@ -916,90 +913,71 @@ + return; + } + +- /* Figure out whether or not we are in "monochromatic" mode. */ +- w_digit = mira_digitize(master.w, master.wave_tol); +- number_of_wavelengths = numberof(w_digit.value); +- if (number_of_wavelengths > 1) { +- monochromatic = (master.monochromatic_option ? 1n : 0n); +- w = w_digit.value; +- } else { +- monochromatic = 1n; +- w = w_digit.value(1); +- } +- h_set, master, w = w, monochromatic = monochromatic; +- +- + /* + ** Make a list of "unique" coordinates using a *slow* O(N^2) algorithm. + */ + +- if (monochromatic) { +- +- local u_inp, v_inp; +- eq_nocopy, u_inp, master.u; +- eq_nocopy, v_inp, master.v; +- number = numberof(u_inp); +- u_out = array(double, number); /* maximum size */ +- v_out = array(double, number); /* maximum size */ +- n_out = array(long, number); /* maximum size */ +- idx = array(long, number); +- sgn = array(long, number); +- mid_wavelength = 0.5*(max(master.w) + min(master.w)); +- freq_tol = master.base_tol/mid_wavelength; +- +- j = k = 1; +- u_out(k) = u_inp(j); +- v_out(k) = v_inp(j); +- n_out(k) = 1; +- idx(j) = k; +- sgn(j) = 1; +- while (++j <= number) { +- +- /* Get j-th position. */ +- u = u_inp(j); +- v = v_inp(j); +- +- /* Search +/-position among list of positions. */ +- u_tmp = u_out(1:k); +- v_tmp = v_out(1:k); +- rp = (temp = u - u_tmp)*temp + (temp = v - v_tmp)*temp; +- rn = (temp = u + u_tmp)*temp + (temp = v + v_tmp)*temp; +- rp_min = min(rp); +- rn_min = min(rn); +- if (min(rp_min, rn_min) > freq_tol) { +- /* Got a new position. */ +- idx(j) = ++k; +- sgn(j) = 1; +- u_out(k) = u; +- v_out(k) = v; +- n_out(k) = 1; +- } else if (rp_min <= rn_min) { +- idx(j) = (kp = rp(mnx)); +- sgn(j) = 1; +- np1 = (n = n_out(kp)) + 1; +- u_out(kp) = (n*u_out(kp) + u)/np1; +- v_out(kp) = (n*v_out(kp) + v)/np1; +- n_out(kp) = np1; +- } else { +- idx(j) = (kp = rn(mnx)); +- sgn(j) = 1; +- np1 = (n = n_out(kp)) + 1; +- u_out(kp) = (n*u_out(kp) - u)/np1; +- v_out(kp) = (n*v_out(kp) - v)/np1; +- n_out(kp) = np1; +- } +- } +- if (k < number) { +- u_out = u_out(1:k); +- v_out = v_out(1:k); +- n_out = n_out(1:k); ++ local u_inp, v_inp; ++ eq_nocopy, u_inp, master.u; ++ eq_nocopy, v_inp, master.v; ++ number = numberof(u_inp); ++ u_out = array(double, number); /* maximum size */ ++ v_out = array(double, number); /* maximum size */ ++ n_out = array(long, number); /* maximum size */ ++ idx = array(long, number); ++ sgn = array(long, number); ++ mid_wavelength = 0.5*(max(master.w) + min(master.w)); ++ freq_tol = master.base_tol/mid_wavelength; ++ ++ j = k = 1; ++ u_out(k) = u_inp(j); ++ v_out(k) = v_inp(j); ++ n_out(k) = 1; ++ idx(j) = k; ++ sgn(j) = 1; ++ while (++j <= number) { ++ ++ /* Get j-th position. */ ++ u = u_inp(j); ++ v = v_inp(j); ++ ++ /* Search +/-position among list of positions. */ ++ u_tmp = u_out(1:k); ++ v_tmp = v_out(1:k); ++ rp = (temp = u - u_tmp)*temp + (temp = v - v_tmp)*temp; ++ rn = (temp = u + u_tmp)*temp + (temp = v + v_tmp)*temp; ++ rp_min = min(rp); ++ rn_min = min(rn); ++ if (min(rp_min, rn_min) > freq_tol) { ++ /* Got a new position. */ ++ idx(j) = ++k; ++ sgn(j) = 1; ++ u_out(k) = u; ++ v_out(k) = v; ++ n_out(k) = 1; ++ } else if (rp_min <= rn_min) { ++ idx(j) = (kp = rp(mnx)); ++ sgn(j) = 1; ++ np1 = (n = n_out(kp)) + 1; ++ u_out(kp) = (n*u_out(kp) + u)/np1; ++ v_out(kp) = (n*v_out(kp) + v)/np1; ++ n_out(kp) = np1; ++ } else { ++ idx(j) = (kp = rn(mnx)); ++ sgn(j) = 1; ++ np1 = (n = n_out(kp)) + 1; ++ u_out(kp) = (n*u_out(kp) - u)/np1; ++ v_out(kp) = (n*v_out(kp) - v)/np1; ++ n_out(kp) = np1; + } +- write, format="There are %d sampled frequencies out of %d measurements.\n", +- k, number; +- +- } else { +- error, "only monochromatic mode is implemented by MiRA"; + } ++ if (k < number) { ++ u_out = u_out(1:k); ++ v_out = v_out(1:k); ++ n_out = n_out(1:k); ++ } ++ write, format="There are %d sampled frequencies out of %d measurements.\n", ++ k, number; + + + /* +@@ -4002,6 +3980,9 @@ + w = mira_get_w(dat); + x = mira_get_x(dat); + y = mira_get_y(dat); ++ if (naxis3 == 1) { ++ w = median(w); ++ } + if (naxis1 != numberof(x) || + naxis2 != numberof(y) || + naxis3 != numberof(w)) { diff -Nru yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/series yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/series --- yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/series 2017-01-25 12:30:39.000000000 +0100 +++ yorick-mira-1.1.0+git20170124.3bd1c3~dfsg1/debian/patches/series 2017-03-05 10:54:17.000000000 +0100 @@ -3,3 +3,4 @@ rgl_needs_yeti bin-mira-path demo-maxeval +monochromatic-doesnt-work
